Microarray Analysis Script for Affymetrix MoGene-1_0-st-v1 using APT (Affymetrix Power Tools) with plier_gcbg normalization and limma. Data already without Probe9 so KO6_4

Install packages only ONCE! if (!requireNamespace(“BiocManager”)) install.packages(“BiocManager”) BiocManager::install(c( “oligo”, “limma”, “pd.mogene.1.0.st.v1”, “mogene10sttranscriptcluster.db”, “AnnotationDbi”, “pheatmap”, “ggplot2”, “ggrepel”, “fgsea”, “gprofiler2”, “topGO”, “org.Mm.eg.db”, “GO.db”, “gtools”, “rmarkdown” )) BiocManager::install(“Rgraphviz”) BiocManager::install(“tidyverse”) Load libraries

library(pd.mogene.1.0.st.v1)
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library(Rgraphviz)
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library(oligo)
library(limma)
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library(AnnotationDbi)
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library(mogene10sttranscriptcluster.db)
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library(pheatmap)
library(ggplot2)
library(ggrepel)
library(fgsea)
library(gprofiler2)
library(topGO)
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library(org.Mm.eg.db)
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library(igraph)
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Creating results folders

dir.create("results", showWarnings = FALSE)
dir.create("results/plots", showWarnings = FALSE)
dir.create("results/tables", showWarnings = FALSE)
dir.create("results/report", showWarnings = FALSE)

Loading expression data after plier-gcbg normalization with APT

plier_gcbg <- read.table("../after_plier-gcbg_apt.txt", sep = "\t", header = TRUE, stringsAsFactors = FALSE, row.names=1)
head(plier_gcbg)
##          Probe10_MoGene.1_0.st.v1.CEL Probe1_MoGene.1_0.st.v1.CEL
## 10338001                   5214.84368                  8551.04834
## 10338002                    380.86360                   436.23978
## 10338003                   1765.73652                  3213.52305
## 10338004                    925.23751                  1801.00505
## 10338005                      3.72918                     4.86664
## 10338006                      6.52560                     7.83556
##          Probe2_MoGene.1_0.st.v1.CEL Probe3_MoGene.1_0.st.v1.CEL
## 10338001                  6906.92956                  5808.41827
## 10338002                   411.18993                   395.80109
## 10338003                  2505.77465                  1883.42023
## 10338004                  1428.19626                  1070.28511
## 10338005                     4.50069                     3.78677
## 10338006                     8.78201                     6.72858
##          Probe4_MoGene.1_0.st.v1.CEL Probe5_MoGene.1_0.st.v1.CEL
## 10338001                  5395.24590                  7036.96409
## 10338002                   403.04392                   419.90256
## 10338003                  1741.93935                  2597.90603
## 10338004                  1007.94946                  1419.30711
## 10338005                     4.12863                     3.78353
## 10338006                     6.40796                     6.60167
##          Probe6_MoGene.1_0.st.v1.CEL Probe7_MoGene.1_0.st.v1.CEL
## 10338001                  4948.37600                  6949.96359
## 10338002                   311.14790                   478.52343
## 10338003                  1649.83037                  2554.77039
## 10338004                   895.16164                  1427.63743
## 10338005                     3.41210                     4.28293
## 10338006                     5.44459                     7.51203
##          Probe8_MoGene.1_0.st.v1.CEL
## 10338001                  6934.13622
## 10338002                   455.42734
## 10338003                  2525.69117
## 10338004                  1295.26136
## 10338005                     2.25587
## 10338006                     6.03033

Removing MoGene.1_0.st.v1 from samples names

colnames(plier_gcbg)  <- gsub('_.*CEL', '\\', colnames(plier_gcbg))
colnames(plier_gcbg)
## [1] "Probe10" "Probe1"  "Probe2"  "Probe3"  "Probe4"  "Probe5"  "Probe6" 
## [8] "Probe7"  "Probe8"

Fix sample name order: Probe1 to Probe10 in numeric order

correct_order <- mixedsort(colnames(plier_gcbg))
correct_order
## [1] "Probe1"  "Probe2"  "Probe3"  "Probe4"  "Probe5"  "Probe6"  "Probe7" 
## [8] "Probe8"  "Probe10"
plier_gcbg <- plier_gcbg[, correct_order]
head(plier_gcbg)
##              Probe1     Probe2     Probe3     Probe4     Probe5     Probe6
## 10338001 8551.04834 6906.92956 5808.41827 5395.24590 7036.96409 4948.37600
## 10338002  436.23978  411.18993  395.80109  403.04392  419.90256  311.14790
## 10338003 3213.52305 2505.77465 1883.42023 1741.93935 2597.90603 1649.83037
## 10338004 1801.00505 1428.19626 1070.28511 1007.94946 1419.30711  895.16164
## 10338005    4.86664    4.50069    3.78677    4.12863    3.78353    3.41210
## 10338006    7.83556    8.78201    6.72858    6.40796    6.60167    5.44459
##              Probe7     Probe8    Probe10
## 10338001 6949.96359 6934.13622 5214.84368
## 10338002  478.52343  455.42734  380.86360
## 10338003 2554.77039 2525.69117 1765.73652
## 10338004 1427.63743 1295.26136  925.23751
## 10338005    4.28293    2.25587    3.72918
## 10338006    7.51203    6.03033    6.52560

Renaming samples from Probe to KO5, KO6 schema

colnames(plier_gcbg) <- c(paste0("KO5_", 1:5), paste0("KO6_", 1:3), "KO6_5")
head(plier_gcbg)
##               KO5_1      KO5_2      KO5_3      KO5_4      KO5_5      KO6_1
## 10338001 8551.04834 6906.92956 5808.41827 5395.24590 7036.96409 4948.37600
## 10338002  436.23978  411.18993  395.80109  403.04392  419.90256  311.14790
## 10338003 3213.52305 2505.77465 1883.42023 1741.93935 2597.90603 1649.83037
## 10338004 1801.00505 1428.19626 1070.28511 1007.94946 1419.30711  895.16164
## 10338005    4.86664    4.50069    3.78677    4.12863    3.78353    3.41210
## 10338006    7.83556    8.78201    6.72858    6.40796    6.60167    5.44459
##               KO6_2      KO6_3      KO6_5
## 10338001 6949.96359 6934.13622 5214.84368
## 10338002  478.52343  455.42734  380.86360
## 10338003 2554.77039 2525.69117 1765.73652
## 10338004 1427.63743 1295.26136  925.23751
## 10338005    4.28293    2.25587    3.72918
## 10338006    7.51203    6.03033    6.52560

Logarithmic transformatioon of the data

plier_gcbg_log <- log2(plier_gcbg)
head(plier_gcbg_log)
##              KO5_1     KO5_2     KO5_3     KO5_4     KO5_5     KO6_1     KO6_2
## 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739 12.762790
## 10338002  8.768978  8.683661  8.628632  8.654793  8.713911  8.281457  8.902446
## 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102 11.318978
## 10338004 10.814587 10.479979 10.063779  9.977208 10.470971  9.806004 10.479414
## 10338005  2.282926  2.170146  1.920968  2.045663  1.919733  1.770660  2.098598
## 10338006  2.970036  3.134551  2.750302  2.679865  2.722831  2.444823  2.909203
##              KO6_3     KO6_5
## 10338001 12.759500 12.348408
## 10338002  8.831077  8.573131
## 10338003 11.302463 10.786054
## 10338004 10.339028  9.853680
## 10338005  1.173684  1.898858
## 10338006  2.592237  2.706111
str(plier_gcbg_log)
## 'data.frame':    35556 obs. of  9 variables:
##  $ KO5_1: num  13.06 8.77 11.65 10.81 2.28 ...
##  $ KO5_2: num  12.75 8.68 11.29 10.48 2.17 ...
##  $ KO5_3: num  12.5 8.63 10.88 10.06 1.92 ...
##  $ KO5_4: num  12.4 8.65 10.77 9.98 2.05 ...
##  $ KO5_5: num  12.78 8.71 11.34 10.47 1.92 ...
##  $ KO6_1: num  12.27 8.28 10.69 9.81 1.77 ...
##  $ KO6_2: num  12.8 8.9 11.3 10.5 2.1 ...
##  $ KO6_3: num  12.76 8.83 11.3 10.34 1.17 ...
##  $ KO6_5: num  12.35 8.57 10.79 9.85 1.9 ...

Changing values lower than 0 to 0

plier_gcbg_log[plier_gcbg_log < 0] <- 0
min(plier_gcbg_log)
## [1] 0
max(plier_gcbg_log)
## [1] 14.8902

Histogram of signal intensities

hist(unlist(plier_gcbg_log), breaks = 100, col = "lightgray",
     main = "Histogram intensywności apt (log2)",
     xlab = "log2 intensywności")

Checking how many probes with 0 values

plier_gcbg_log_no_zero_rows <- plier_gcbg_log[!apply(plier_gcbg_log == 0, 1, all), ]
str(plier_gcbg_log_no_zero_rows)
## 'data.frame':    35552 obs. of  9 variables:
##  $ KO5_1: num  13.06 8.77 11.65 10.81 2.28 ...
##  $ KO5_2: num  12.75 8.68 11.29 10.48 2.17 ...
##  $ KO5_3: num  12.5 8.63 10.88 10.06 1.92 ...
##  $ KO5_4: num  12.4 8.65 10.77 9.98 2.05 ...
##  $ KO5_5: num  12.78 8.71 11.34 10.47 1.92 ...
##  $ KO6_1: num  12.27 8.28 10.69 9.81 1.77 ...
##  $ KO6_2: num  12.8 8.9 11.3 10.5 2.1 ...
##  $ KO6_3: num  12.76 8.83 11.3 10.34 1.17 ...
##  $ KO6_5: num  12.35 8.57 10.79 9.85 1.9 ...
plier_gcbg_log_zero_rows <- plier_gcbg_log[apply(plier_gcbg_log == 0, 1, all), ]
str(plier_gcbg_log_zero_rows)
## 'data.frame':    4 obs. of  9 variables:
##  $ KO5_1: num  0 0 0 0
##  $ KO5_2: num  0 0 0 0
##  $ KO5_3: num  0 0 0 0
##  $ KO5_4: num  0 0 0 0
##  $ KO5_5: num  0 0 0 0
##  $ KO6_1: num  0 0 0 0
##  $ KO6_2: num  0 0 0 0
##  $ KO6_3: num  0 0 0 0
##  $ KO6_5: num  0 0 0 0
plier_gcbg_log_no_any_zeros <- plier_gcbg_log[!apply(plier_gcbg_log == 0, 1, any), ]
str(plier_gcbg_log_no_any_zeros)
## 'data.frame':    35214 obs. of  9 variables:
##  $ KO5_1: num  13.06 8.77 11.65 10.81 2.28 ...
##  $ KO5_2: num  12.75 8.68 11.29 10.48 2.17 ...
##  $ KO5_3: num  12.5 8.63 10.88 10.06 1.92 ...
##  $ KO5_4: num  12.4 8.65 10.77 9.98 2.05 ...
##  $ KO5_5: num  12.78 8.71 11.34 10.47 1.92 ...
##  $ KO6_1: num  12.27 8.28 10.69 9.81 1.77 ...
##  $ KO6_2: num  12.8 8.9 11.3 10.5 2.1 ...
##  $ KO6_3: num  12.76 8.83 11.3 10.34 1.17 ...
##  $ KO6_5: num  12.35 8.57 10.79 9.85 1.9 ...
plier_gcbg_log_any_zeros <- plier_gcbg_log[apply(plier_gcbg_log == 0, 1, any), ]
str(plier_gcbg_log_any_zeros)
## 'data.frame':    342 obs. of  9 variables:
##  $ KO5_1: num  0 0 3.86 3.12 0 ...
##  $ KO5_2: num  1.79 2.29 0 4.41 2.24 ...
##  $ KO5_3: num  1.558 0.677 0.783 0.286 0 ...
##  $ KO5_4: num  0.209 1.175 2.732 1.8 0 ...
##  $ KO5_5: num  0 0 2.08 0 2.25 ...
##  $ KO6_1: num  0.724 1.037 1.034 3.503 0 ...
##  $ KO6_2: num  1.24 0.72 3.31 1.97 2.9 ...
##  $ KO6_3: num  0 0 0.691 3.993 0 ...
##  $ KO6_5: num  0.32 0 0.549 2.749 0 ...
min(plier_gcbg_log_any_zeros)
## [1] 0
max(plier_gcbg_log_any_zeros)
## [1] 10.67655

Histogram of signal intensities of probes with any zero value

hist(unlist(plier_gcbg_log_any_zeros), breaks = 100, col = "lightgray",
     main = "Histogram intensywności apt (log2) any0",
     xlab = "log2 intensywności")

Boxplot of probes with any zero value

boxplot(plier_gcbg_log_any_zeros, las = 2, main = "Boxplot po normalizacji (RMA) all", col = "lightblue")

Removing probes with zero value in any sample

plier_gcbg_log <- plier_gcbg_log_no_any_zeros

Boxplot all rows

boxplot(plier_gcbg_log, las = 2, main = "Boxplot po normalizacji (RMA) noany0", col = "lightblue")

PCA with probes without zeros in any sample

group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
pca <- prcomp(t(plier_gcbg_log))
group_colors <- ifelse(group == "KO5", "blue", "red")
plot(pca$x[,1:2], col = group_colors, pch = 19,
     main = "PCA after APT any0", xlab = "PC1", ylab = "PC2")
text(pca$x[,1], pca$x[,2], labels = colnames(plier_gcbg), pos = 3, cex = 0.8)
legend("topright", legend = levels(group), col = c("blue", "red"), pch = 19)

Correlation between samples

cor_matrix <- cor(plier_gcbg_log)
pheatmap(cor_matrix, main = "Korelacja między próbkami")

Samples dendrogram

sample_distF <- dist(t(plier_gcbg_log))
hc <- hclust(sample_distF)
plot(hc, labels = colnames(plier_gcbg), main = "Sample clustering (hierarchical)", xlab = "", sub = "")

Median expression per sample

mediansF <- apply(plier_gcbg_log, 2, median)
barplot(mediansF, names.arg = colnames(plier_gcbg), las = 2,
        col = group_colors, main = "Median expression per sample")

Calculating variation of all genes

varsF <- apply(plier_gcbg_log, 1, var)

Heatmap expresison of 100 most variable genes

top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:100]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
         annotation_col = annotation_col,
         show_rownames = FALSE,
         main = "Heatmap of top 100 variable genes")

Heatmap expresison of 500 most variable genes

top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:500]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
         annotation_col = annotation_col,
         show_rownames = FALSE,
         main = "Heatmap of top 500 variable genes")

Heatmap expresison of 1000 most variable genes

top_var_genesF <- names(sort(varsF, decreasing = TRUE))[1:1000]
expr_topvarF <- plier_gcbg_log[top_var_genesF, ]
group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(expr_topvarF)
pheatmap(expr_topvarF, scale = "row",
         annotation_col = annotation_col,
         show_rownames = FALSE,
         main = "Heatmap of top 1000 variable genes")

Euclidan distance between samples

sample_distF <- dist(t(plier_gcbg_log))
sample_dist_matF <- as.matrix(sample_distF)
pheatmap(sample_dist_matF, main = "Sample-to-sample Euclidean distance")

Checking knockout, stable and backgroud genes expression Loading oryginal annotation from mogene10sttranscriptcluster.db

annot_old_exprsF <- select(mogene10sttranscriptcluster.db,
                           keys = rownames(plier_gcbg_log),
                           columns = c("SYMBOL"),
                           keytype = "PROBEID")
## 'select()' returned 1:many mapping between keys and columns
head(annot_old_exprsF)
##    PROBEID SYMBOL
## 1 10338001   <NA>
## 2 10338002   <NA>
## 3 10338003   <NA>
## 4 10338004   <NA>
## 5 10338005   <NA>
## 6 10338006   <NA>
str(annot_old_exprsF)
## 'data.frame':    46425 obs. of  2 variables:
##  $ PROBEID: chr  "10338001" "10338002" "10338003" "10338004" ...
##  $ SYMBOL : chr  NA NA NA NA ...

Merging original annotation with expression matrix by ProbeID

exprsF_annot_old <- merge(plier_gcbg_log, annot_old_exprsF, by.x = "row.names", by.y = "PROBEID")

Renaming rownames columnn to ProbeID

colnames(exprsF_annot_old)[1] <- "ProbeID"
head(exprsF_annot_old)
##    ProbeID     KO5_1     KO5_2     KO5_3     KO5_4     KO5_5     KO6_1
## 1 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739
## 2 10338002  8.768978  8.683661  8.628632  8.654793  8.713911  8.281457
## 3 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102
## 4 10338004 10.814587 10.479979 10.063779  9.977208 10.470971  9.806004
## 5 10338005  2.282926  2.170146  1.920968  2.045663  1.919733  1.770660
## 6 10338006  2.970036  3.134551  2.750302  2.679865  2.722831  2.444823
##       KO6_2     KO6_3     KO6_5 SYMBOL
## 1 12.762790 12.759500 12.348408   <NA>
## 2  8.902446  8.831077  8.573131   <NA>
## 3 11.318978 11.302463 10.786054   <NA>
## 4 10.479414 10.339028  9.853680   <NA>
## 5  2.098598  1.173684  1.898858   <NA>
## 6  2.909203  2.592237  2.706111   <NA>
str(exprsF_annot_old)
## 'data.frame':    46425 obs. of  11 variables:
##  $ ProbeID: chr  "10338001" "10338002" "10338003" "10338004" ...
##  $ KO5_1  : num  13.06 8.77 11.65 10.81 2.28 ...
##  $ KO5_2  : num  12.75 8.68 11.29 10.48 2.17 ...
##  $ KO5_3  : num  12.5 8.63 10.88 10.06 1.92 ...
##  $ KO5_4  : num  12.4 8.65 10.77 9.98 2.05 ...
##  $ KO5_5  : num  12.78 8.71 11.34 10.47 1.92 ...
##  $ KO6_1  : num  12.27 8.28 10.69 9.81 1.77 ...
##  $ KO6_2  : num  12.8 8.9 11.3 10.5 2.1 ...
##  $ KO6_3  : num  12.76 8.83 11.3 10.34 1.17 ...
##  $ KO6_5  : num  12.35 8.57 10.79 9.85 1.9 ...
##  $ SYMBOL : chr  NA NA NA NA ...

Loading Knockout genes

genes_of_interest <- c("Acr", "Tnp2", "H1f6", "Spmap2", "Creb3l4", "Tex22")

Creating a subset table with genes of interest

subset_genes_table <- exprsF_annot_old[exprsF_annot_old$SYMBOL %in% genes_of_interest, ]
subset_genes_table_unique <- subset_genes_table[!duplicated(subset_genes_table$SYMBOL), ]

Making expression plot of knockout genes

df_long <- subset_genes_table_unique %>%
  pivot_longer(cols = starts_with("KO"),
               names_to = "Sample",
               values_to = "Expression") %>%
  mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))

ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = SYMBOL, color = SYMBOL)) +
  geom_line(size = 1) +
  geom_point(size = 2) +
  theme_minimal() +
  labs(title = "Ekspresja genów w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
ggsave("results/plots/Knockout_genes_expression_plot_apt.jpg", ala)
## Saving 7 x 5 in image
ala

write.csv(subset_genes_table, "results/tables/Knockout_genes_table_apt.csv", row.names = FALSE)

Loading reference genes for testis plus CcDS33 and Pxt1

genes_of_interest1 <- c("Ccdc33", "Pxt1", "Gapdh", "Actb", "Hprt", "Ppia", "Polr2a", "Rpl13a", "Ywhaz", "Tbp", "18srRNA", "Sdha")

Creating a subset table with genes of interest

subset_genes_table1 <- exprsF_annot_old[exprsF_annot_old$SYMBOL %in% genes_of_interest1, ]
subset_genes_table_unique1 <- subset_genes_table1[!duplicated(subset_genes_table1$SYMBOL), ]

Making expresison plot

df_long <- subset_genes_table_unique1 %>%
  pivot_longer(cols = starts_with("KO"),
               names_to = "Sample",
               values_to = "Expression") %>%
  mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))

ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = SYMBOL, color = SYMBOL)) +
  geom_line(size = 1) +
  geom_point(size = 2) +
  theme_minimal() +
  labs(title = "Ekspresja genów w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

ggsave("results/plots/reference_genes_testis_apt.jpg", ala)
## Saving 7 x 5 in image
ala

write.csv(subset_genes_table1, "results/tables/subset_genes_table_apt1.csv", row.names = FALSE)

Loading background probes

background_probes <- read.table("../bcg.probes", header = FALSE, stringsAsFactors = FALSE)

Renaming rownames column to ProbeID

colnames(background_probes) <- "PROBEID"
head(exprsF_annot_old)
##    ProbeID     KO5_1     KO5_2     KO5_3     KO5_4     KO5_5     KO6_1
## 1 10338001 13.061886 12.753829 12.503930 12.397473 12.780737 12.272739
## 2 10338002  8.768978  8.683661  8.628632  8.654793  8.713911  8.281457
## 3 10338003 11.649940 11.291041 10.879139 10.766479 11.343134 10.688102
## 4 10338004 10.814587 10.479979 10.063779  9.977208 10.470971  9.806004
## 5 10338005  2.282926  2.170146  1.920968  2.045663  1.919733  1.770660
## 6 10338006  2.970036  3.134551  2.750302  2.679865  2.722831  2.444823
##       KO6_2     KO6_3     KO6_5 SYMBOL
## 1 12.762790 12.759500 12.348408   <NA>
## 2  8.902446  8.831077  8.573131   <NA>
## 3 11.318978 11.302463 10.786054   <NA>
## 4 10.479414 10.339028  9.853680   <NA>
## 5  2.098598  1.173684  1.898858   <NA>
## 6  2.909203  2.592237  2.706111   <NA>

Creating a subset table with background probes

subset_bcg_table <- exprsF_annot_old[exprsF_annot_old$ProbeID %in% background_probes$PROBEID, ]

df_long <- subset_bcg_table %>%
  pivot_longer(cols = starts_with("KO"),
               names_to = "Sample",
               values_to = "Expression") %>%
  mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))

ala <- ggplot(df_long, aes(x = Sample, y = Expression, group = ProbeID, color = ProbeID)) +
  geom_line(size = 1) +
  geom_point(size = 2) +
  theme_minimal() +
  labs(title = "Ekspresja sond tła w próbkach KO5 i KO6", y = "log2(Expression)", x = "") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

ggsave("results/plots/BckgProbesets_apt.jpg", ala)
## Saving 7 x 5 in image
ala

write.csv(subset_genes_table1, "results/tables/BckProbes_apt.csv", row.names = FALSE)

Checking probesests by variation and expression Calculating variation and mean expression per probeset

gene_var <- apply(plier_gcbg_log, 1, var)
gene_mean <- rowMeans(plier_gcbg_log)

Defining low and high variation threshlods

low_var_genes <- which(gene_var <= 0.01)
high_var_genes <- which(gene_var > 0.01)
length(low_var_genes)
## [1] 5055
length(high_var_genes)
## [1] 30159

Randomly get 100 probesets with low and high variation

set.seed(42)  #' dla powtarzalności
low_sample <- sample(low_var_genes, 100)
high_sample <- sample(high_var_genes, 100)

Plotting expression of low and high variation probes

df_long_var <- bind_rows(
  plier_gcbg_log[low_sample, ] %>% 
    as.data.frame() %>%
    mutate(VarGroup = "LowVar", ProbeID = rownames(.)),
  
  plier_gcbg_log[high_sample, ] %>%
    as.data.frame() %>%
    mutate(VarGroup = "HighVar", ProbeID = rownames(.))
) %>%
  pivot_longer(cols = starts_with("KO"),
               names_to = "Sample",
               values_to = "Expression") %>%
  mutate(Group = ifelse(grepl("KO5", Sample), "KO5", "KO6"))

p_lines <- ggplot(df_long_var, aes(x = Sample, y = Expression, group = ProbeID)) +
  geom_line(aes(color = Group), alpha = 0.4) +
  facet_wrap(~VarGroup, scales = "free_y") +
  theme_minimal() +
  labs(title = "Ekspresja każdej sondy (LowVar / HighVar) w KO5 vs KO6", x = "", y = "log2(Expression)") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
  scale_color_manual(values = c("KO5" = "blue", "KO6" = "red"))

ggsave("results/plots/Variationwise_expression_Probes_KO5vsKO6_apt.jpg", p_lines, width = 10, height = 6)

p_lines

How many high variable genes has expression higher than:

for (i in 2:10) {
  print(paste("High variable probesest with expression higher than", i," : ", sum(gene_mean[high_var_genes] >= i)))
}
## [1] "High variable probesest with expression higher than 2  :  30139"
## [1] "High variable probesest with expression higher than 3  :  30080"
## [1] "High variable probesest with expression higher than 4  :  29868"
## [1] "High variable probesest with expression higher than 5  :  29223"
## [1] "High variable probesest with expression higher than 6  :  27585"
## [1] "High variable probesest with expression higher than 7  :  23797"
## [1] "High variable probesest with expression higher than 8  :  16932"
## [1] "High variable probesest with expression higher than 9  :  10604"
## [1] "High variable probesest with expression higher than 10  :  6036"

Filtering based on variantion and expression higher than threshold in at leat one of the compared groups Separating columns of comparisons groups

ko5_cols <- grep("^KO5", colnames(plier_gcbg_log))
ko6_cols <- grep("^KO6", colnames(plier_gcbg_log))

Calculating mean expresison per group

ko5_mean <- rowMeans(plier_gcbg_log[, ko5_cols])
ko6_mean <- rowMeans(plier_gcbg_log[, ko6_cols])

Calculating variation per group

ko5_var <- apply(plier_gcbg_log[, ko5_cols], 1, var)
ko6_var <- apply(plier_gcbg_log[, ko6_cols], 1, var)

Setting thresholds Threshold of 8 instead of 10 was decideded by looking at expression values after plier_gcbg normalization by Affymetrix Power Toools, which makes the normalization using background antigenomic probes on the chip (abs(ko5_mean - ko6_mean) >= .5) & #’ I am not adding this threshiold of expression difference beteen groups

keep <- ((ko5_mean >= 8) | (ko6_mean >= 8)) & 
  ((ko5_var > 0.01) | (ko6_var > 0.01))

Filtering by thresholds

plier_gcbg_log_filtered <- plier_gcbg_log[keep, ]

How many left

str(plier_gcbg_log_filtered)
## 'data.frame':    17883 obs. of  9 variables:
##  $ KO5_1: num  13.06 8.77 11.65 10.81 9.98 ...
##  $ KO5_2: num  12.75 8.68 11.29 10.48 9.96 ...
##  $ KO5_3: num  12.5 8.63 10.88 10.06 9.69 ...
##  $ KO5_4: num  12.4 8.65 10.77 9.98 9.69 ...
##  $ KO5_5: num  12.78 8.71 11.34 10.47 10.09 ...
##  $ KO6_1: num  12.27 8.28 10.69 9.81 9.51 ...
##  $ KO6_2: num  12.8 8.9 11.3 10.5 10 ...
##  $ KO6_3: num  12.76 8.83 11.3 10.34 9.9 ...
##  $ KO6_5: num  12.35 8.57 10.79 9.85 9.41 ...

DE Analysis

group <- factor(c(rep("KO5", 5), rep("KO6", 4)))
group_levels <- levels(group)
group_levels
## [1] "KO5" "KO6"
design <- model.matrix(~ group)
design
##   (Intercept) groupKO6
## 1           1        0
## 2           1        0
## 3           1        0
## 4           1        0
## 5           1        0
## 6           1        1
## 7           1        1
## 8           1        1
## 9           1        1
## attr(,"assign")
## [1] 0 1
## attr(,"contrasts")
## attr(,"contrasts")$group
## [1] "contr.treatment"
fitF <- lmFit(plier_gcbg_log_filtered, design)
fitF <- eBayes(fitF)

Histogram of Mean expressions

hist(fitF$Amean)

plotSA(fitF)

DE results table

resultsF <- topTable(fitF, coef = 2, number = Inf, confint = TRUE)
write.csv(resultsF, "results/tables/results_apt.csv", row.names = FALSE)
head(resultsF)
##              logFC      CI.L      CI.R  AveExpr         t      P.Value
## 10389130 -4.288114 -4.556269 -4.019959 8.741076 -34.42180 1.565020e-14
## 10542414  3.703390  3.465927  3.940852 8.645955  33.57049 2.185547e-14
## 10398966 -4.106109 -4.456084 -3.756133 8.843426 -25.25495 9.578656e-13
## 10375121  2.172477  1.959804  2.385150 9.614721  21.98853 5.945455e-12
## 10375123  2.086027  1.879303  2.292752 9.589559  21.72110 6.982184e-12
## 10522127  1.334423  1.071793  1.597054 8.170186  10.93710 4.423838e-08
##             adj.P.Val         B
## 10389130 1.954207e-10 17.082041
## 10542414 1.954207e-10 16.980163
## 10398966 5.709837e-09 15.556675
## 10375121 2.497248e-08 14.676819
## 10375123 2.497248e-08 14.593079
## 10522127 1.318525e-04  8.582618
str(resultsF)
## 'data.frame':    17883 obs. of  8 variables:
##  $ logFC    : num  -4.29 3.7 -4.11 2.17 2.09 ...
##  $ CI.L     : num  -4.56 3.47 -4.46 1.96 1.88 ...
##  $ CI.R     : num  -4.02 3.94 -3.76 2.39 2.29 ...
##  $ AveExpr  : num  8.74 8.65 8.84 9.61 9.59 ...
##  $ t        : num  -34.4 33.6 -25.3 22 21.7 ...
##  $ P.Value  : num  1.57e-14 2.19e-14 9.58e-13 5.95e-12 6.98e-12 ...
##  $ adj.P.Val: num  1.95e-10 1.95e-10 5.71e-09 2.50e-08 2.50e-08 ...
##  $ B        : num  17.1 17 15.6 14.7 14.6 ...

Adnotation with Original mogene10sttranscriptcluster.db Loading Original Annotation

annot_old1 <- select(mogene10sttranscriptcluster.db,
                     keys = rownames(resultsF),
                     columns = c("SYMBOL", "ENSEMBL"),
                     keytype = "PROBEID")
## 'select()' returned 1:many mapping between keys and columns
str(annot_old1)
## 'data.frame':    24881 obs. of  3 variables:
##  $ PROBEID: chr  "10389130" "10542414" "10398966" "10375121" ...
##  $ SYMBOL : chr  "Slfn5os" "Ptpro" "Tex22" NA ...
##  $ ENSEMBL: chr  "ENSMUSG00000086327" "ENSMUSG00000030223" "ENSMUSG00000012211" NA ...
head(annot_old1)
##    PROBEID  SYMBOL            ENSEMBL
## 1 10389130 Slfn5os ENSMUSG00000086327
## 2 10542414   Ptpro ENSMUSG00000030223
## 3 10398966   Tex22 ENSMUSG00000012211
## 4 10375121    <NA>               <NA>
## 5 10375123    <NA>               <NA>
## 6 10522127     Klb ENSMUSG00000029195

number of probes with more than one adnotation

sum(duplicated(annot_old1$PROBEID))
## [1] 6998

Merging DE results with Original Annotation table

results_annot_old1 <- merge(resultsF, annot_old1, by.x = "row.names", by.y = "PROBEID")
head(results_annot_old1)
##   Row.names       logFC       CI.L      CI.R   AveExpr          t   P.Value
## 1  10338001 -0.16371142 -0.4764832 0.1490603 12.626810 -1.1266915 0.2795288
## 2  10338002 -0.04296735 -0.2936639 0.2077292  8.670898 -0.3689299 0.7179093
## 3  10338003 -0.16204730 -0.5575564 0.2334618 11.113925 -0.8819397 0.3932628
## 4  10338004 -0.24177318 -0.6292171 0.1456707 10.253850 -1.3432377 0.2013710
## 5  10338009 -0.17007889 -0.4648539 0.1246962  9.806877 -1.2419762 0.2354179
## 6  10338016 -0.09271588 -0.3339338 0.1485020  9.377283 -0.8273671 0.4224330
##   adj.P.Val         B SYMBOL ENSEMBL
## 1 0.5265948 -5.746507   <NA>    <NA>
## 2 0.8567482 -6.308196   <NA>    <NA>
## 3 0.6260209 -5.984502   <NA>    <NA>
## 4 0.4461390 -5.496695   <NA>    <NA>
## 5 0.4818564 -5.617819   <NA>    <NA>
## 6 0.6493075 -6.030613   <NA>    <NA>
str(results_annot_old1)
## 'data.frame':    24881 obs. of  11 variables:
##  $ Row.names: chr  "10338001" "10338002" "10338003" "10338004" ...
##  $ logFC    : num  -0.164 -0.043 -0.162 -0.242 -0.17 ...
##  $ CI.L     : num  -0.476 -0.294 -0.558 -0.629 -0.465 ...
##  $ CI.R     : num  0.149 0.208 0.233 0.146 0.125 ...
##  $ AveExpr  : num  12.63 8.67 11.11 10.25 9.81 ...
##  $ t        : num  -1.127 -0.369 -0.882 -1.343 -1.242 ...
##  $ P.Value  : num  0.28 0.718 0.393 0.201 0.235 ...
##  $ adj.P.Val: num  0.527 0.857 0.626 0.446 0.482 ...
##  $ B        : num  -5.75 -6.31 -5.98 -5.5 -5.62 ...
##  $ SYMBOL   : chr  NA NA NA NA ...
##  $ ENSEMBL  : chr  NA NA NA NA ...

naming rownames column with ProbeID

colnames(results_annot_old1)[1] <- "ProbeID"

filtering out rows without SYMBOL or ENSEMBL

results_annot_old1 <- results_annot_old1 %>%
  filter(
    (!is.na(SYMBOL) & SYMBOL != "") |
      (!is.na(ENSEMBL) & ENSEMBL != "")
  )

str(results_annot_old1)
## 'data.frame':    20188 obs. of  11 variables:
##  $ ProbeID  : chr  "10344624" "10344633" "10344637" "10344658" ...
##  $ logFC    : num  -0.118 -0.0337 -0.0848 -0.0362 -0.2313 ...
##  $ CI.L     : num  -0.292 -0.221 -0.275 -0.227 -0.416 ...
##  $ CI.R     : num  0.0565 0.1536 0.1052 0.1549 -0.0465 ...
##  $ AveExpr  : num  12.08 11.36 11.12 12.33 9.78 ...
##  $ t        : num  -1.455 -0.387 -0.961 -0.408 -2.695 ...
##  $ P.Value  : num  0.1685 0.7048 0.3536 0.6898 0.0179 ...
##  $ adj.P.Val: num  0.411 0.848 0.595 0.84 0.168 ...
##  $ B        : num  -5.35 -6.3 -5.91 -6.29 -3.37 ...
##  $ SYMBOL   : chr  "Lypla1" "Tcea1" "Atp6v1h" "Rb1cc1" ...
##  $ ENSEMBL  : chr  "ENSMUSG00000025903" "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" ...
head(results_annot_old1)
##    ProbeID       logFC       CI.L        CI.R   AveExpr          t    P.Value
## 1 10344624 -0.11796296 -0.2924560  0.05653009 12.078768 -1.4551948 0.16850306
## 2 10344633 -0.03365629 -0.2208716  0.15355899 11.362263 -0.3869711 0.70481722
## 3 10344637 -0.08481478 -0.2748344  0.10520485 11.123007 -0.9607860 0.35357609
## 4 10344658 -0.03621075 -0.2273545  0.15493297 12.333149 -0.4077848 0.68983356
## 5 10344707 -0.23134278 -0.4161381 -0.04654740  9.779085 -2.6947498 0.01790379
## 6 10344713 -0.32060534 -0.6176199 -0.02359074  9.898482 -2.3235207 0.03636137
##   adj.P.Val         B  SYMBOL            ENSEMBL
## 1 0.4106491 -5.354516  Lypla1 ENSMUSG00000025903
## 2 0.8480457 -6.301155   Tcea1 ENSMUSG00000033813
## 3 0.5947829 -5.913296 Atp6v1h ENSMUSG00000033793
## 4 0.8395928 -6.292624  Rb1cc1 ENSMUSG00000025907
## 5 0.1684237 -3.368097  Pcmtd1 ENSMUSG00000051285
## 6 0.2162651 -4.021586   Ahcyl ENSMUSG00000048087
write.csv(results_annot_old1, "results/tables/diff_expr_resultsF_oryg_annot.csv", row.names = FALSE)

Checking uniquness of the Probes and Genes How many ENSEMBL with more than 1 Probe

symbol_probe_counts <- results_annot_old1 %>%
  group_by(ENSEMBL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)

nrow(symbol_probe_counts)  
## [1] 1456

How many SYMBOL with more than 1 Probe

symbol_probe_counts <- results_annot_old1 %>%
  group_by(SYMBOL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)

nrow(symbol_probe_counts)  
## [1] 1534

How many Probes mapping to more than 1 ENSEMBL

probe_symbol_counts <- results_annot_old1 %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(ENSEMBL)) %>%
  filter(n_symbols > 1)

nrow(probe_symbol_counts) 
## [1] 1095

How many Probes mapping to more than 1 SYMBOL

probe_symbol_counts <- results_annot_old1 %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(SYMBOL)) %>%
  filter(n_symbols > 1)

nrow(probe_symbol_counts) 
## [1] 1089

Solving problems with Non unique Genes and Probes List of ProbeIDs with more than one gene based on SYMBOL or ENSEMBL

conflict_ids <- results_annot_old1 %>%
  group_by(ProbeID) %>%
  filter(n_distinct(SYMBOL) > 1 | n_distinct(ENSEMBL) > 1) %>%
  pull(ProbeID) %>%
  unique()
length(conflict_ids)
## [1] 1112

Removal of ProbeIDs with nonunique Genes If ProbeID with just 1 row - stays If SYMBOLs with the same ENSEMBL have common core, randomly choose one row. Other way remove rows.

filtered_results_old1 <- results_annot_old1 %>%
  group_by(ProbeID) %>%
  group_modify(~ {
    subdf <- .x
    if (nrow(subdf) == 1) return(subdf)
    
    unique_symbols <- unique(subdf$SYMBOL)
    unique_symbols <- unique_symbols[!is.na(unique_symbols) & unique_symbols != ""]

    unique_ensembls <- unique(subdf$ENSEMBL)
    unique_ensembls <- unique_ensembls[!is.na(unique_ensembls) & unique_ensembls != ""]
    
    roots <- stringr::str_extract(unique_symbols, "^[A-Za-z]{3,}")
    roots <- na.omit(roots)
    
    common_root <- length(roots) > 0 && length(unique(roots)) == 1
    single_valid_ensembl <- length(unique_ensembls) == 1
    
    if (common_root && single_valid_ensembl) {
      return(subdf[sample(nrow(subdf), 1), ])
    } else {
      return(subdf[0, ])
    }
  }) %>%
  ungroup()

str(filtered_results_old1)
## tibble [12,185 × 11] (S3: tbl_df/tbl/data.frame)
##  $ ProbeID  : chr [1:12185] "10344624" "10344633" "10344637" "10344658" ...
##  $ logFC    : num [1:12185] -0.118 -0.0337 -0.0848 -0.0362 -0.2313 ...
##  $ CI.L     : num [1:12185] -0.292 -0.221 -0.275 -0.227 -0.416 ...
##  $ CI.R     : num [1:12185] 0.0565 0.1536 0.1052 0.1549 -0.0465 ...
##  $ AveExpr  : num [1:12185] 12.08 11.36 11.12 12.33 9.78 ...
##  $ t        : num [1:12185] -1.455 -0.387 -0.961 -0.408 -2.695 ...
##  $ P.Value  : num [1:12185] 0.1685 0.7048 0.3536 0.6898 0.0179 ...
##  $ adj.P.Val: num [1:12185] 0.411 0.848 0.595 0.84 0.168 ...
##  $ B        : num [1:12185] -5.35 -6.3 -5.91 -6.29 -3.37 ...
##  $ SYMBOL   : chr [1:12185] "Lypla1" "Tcea1" "Atp6v1h" "Rb1cc1" ...
##  $ ENSEMBL  : chr [1:12185] "ENSMUSG00000025903" "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" ...

Make pairs by SYMBOL

symbol_edges <- filtered_results_old1 %>%
  filter(!is.na(SYMBOL) & SYMBOL != "") %>%
  group_by(SYMBOL) %>%
  filter(n() > 1) %>%
  reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(symbol_edges)
## [1] 3964

Make pairs by ENSEMBL

ensembl_edges <- filtered_results_old1 %>%
  filter(!is.na(ENSEMBL) & ENSEMBL != "") %>%
  group_by(ENSEMBL) %>%
  filter(n() > 1) %>%
  reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(ensembl_edges)
## [1] 3913

Connecting pairs lists

edges <- bind_rows(symbol_edges, ensembl_edges) %>%
  pull(pairs)
length(edges)
## [1] 7877

Making data.frame

edge_df <- do.call(rbind, lapply(edges, function(x) data.frame(from = x[1], to = x[2])))
str(edge_df)
## 'data.frame':    7877 obs. of  2 variables:
##  $ from: chr  "10394783" "10502417" "10394805" "10425651" ...
##  $ to  : chr  "10394786" "10552622" "10394833" "10425653" ...

Creating graph

g <- graph_from_data_frame(edge_df, directed = FALSE)
clusters <- components(g)

Annotatioing genes with clusters

cluster_map <- data.frame(ProbeID = names(clusters$membership),
                          gene_cluster = paste0("C", clusters$membership))

Joining clusters with z ProbeId, ENsembl, Symbol i DE

filtered_results_old1_clustered <- filtered_results_old1 %>%
  left_join(cluster_map, by = "ProbeID") %>%
  mutate(gene_cluster = ifelse(is.na(gene_cluster), paste0("single_", ProbeID), gene_cluster))

Choose bedt ProbeiD by FDR or LogFC

results_genes_unique_old1 <- filtered_results_old1_clustered %>%
  group_by(gene_cluster) %>%
  arrange(adj.P.Val, desc(abs(logFC))) %>%
  summarise(best_row = list(first(cur_data())), .groups = "drop") %>%
  unnest(best_row) %>%
  dplyr::select(-gene_cluster) %>%
  as.data.frame()
## Warning: There was 1 warning in `summarise()`.
## ℹ In argument: `best_row = list(first(cur_data()))`.
## ℹ In group 1: `gene_cluster = "C1"`.
## Caused by warning:
## ! `cur_data()` was deprecated in dplyr 1.1.0.
## ℹ Please use `pick()` instead.
head(results_genes_unique_old1)
##    ProbeID       logFC        CI.L        CI.R   AveExpr          t     P.Value
## 1 10394783  0.41175139 -0.05185455  0.87535733  9.463494  1.9117878 0.077393739
## 2 10531181  0.16846035 -0.02967207  0.36659276  8.059947  1.8301882 0.089414178
## 3 10587627  0.03612688 -0.16509952  0.23735329 10.218247  0.3864552 0.705190280
## 4 10462136 -0.42016703 -0.65071096 -0.18962309 10.383647 -3.9230321 0.001637431
## 5 10448559  0.21358447 -0.09590773  0.52307666  7.927709  1.4855031 0.160416411
## 6 10586250 -0.19381215 -0.41163701  0.02401272  8.952325 -1.9152573 0.076916655
##    adj.P.Val         B        SYMBOL            ENSEMBL
## 1 0.29175480 -4.697095 1700030C10Rik ENSMUSG00000099759
## 2 0.31236447 -4.822682       Adamts3 ENSMUSG00000043635
## 3 0.84827329 -6.301361        Cyb5r4 ENSMUSG00000032872
## 4 0.06313255 -1.094365          Cycs ENSMUSG00000063694
## 5 0.40060420 -5.314608 D330041H03Rik ENSMUSG00000073437
## 6 0.29074203 -4.691687       Dennd4a ENSMUSG00000053641
str(results_genes_unique_old1)
## 'data.frame':    11107 obs. of  11 variables:
##  $ ProbeID  : chr  "10394783" "10531181" "10587627" "10462136" ...
##  $ logFC    : num  0.4118 0.1685 0.0361 -0.4202 0.2136 ...
##  $ CI.L     : num  -0.0519 -0.0297 -0.1651 -0.6507 -0.0959 ...
##  $ CI.R     : num  0.875 0.367 0.237 -0.19 0.523 ...
##  $ AveExpr  : num  9.46 8.06 10.22 10.38 7.93 ...
##  $ t        : num  1.912 1.83 0.386 -3.923 1.486 ...
##  $ P.Value  : num  0.07739 0.08941 0.70519 0.00164 0.16042 ...
##  $ adj.P.Val: num  0.2918 0.3124 0.8483 0.0631 0.4006 ...
##  $ B        : num  -4.7 -4.82 -6.3 -1.09 -5.31 ...
##  $ SYMBOL   : chr  "1700030C10Rik" "Adamts3" "Cyb5r4" "Cycs" ...
##  $ ENSEMBL  : chr  "ENSMUSG00000099759" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000063694" ...
write.csv(results_genes_unique_old1, "results/tables/diff_expr_resultsF_oryg_annot_uniq.csv", row.names = FALSE)

Checking uniquness of Probes and Genes How many ENSEMBL with more than 1 Probe

symbol_probe_counts <- results_genes_unique_old1 %>%
  group_by(ENSEMBL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 1
symbol_probe_counts
## # A tibble: 1 × 2
##   ENSEMBL n_probes
##   <chr>      <int>
## 1 <NA>         186

How many SYMBOL with more than 1 Probe

symbol_probe_counts <- results_genes_unique_old1 %>%
  group_by(SYMBOL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 0
symbol_probe_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: SYMBOL <chr>, n_probes <int>

How many Probes mapping to more than 1 ENSEMBL

probe_symbol_counts <- results_genes_unique_old1 %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(ENSEMBL)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) 
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>
probe_symbol_counts <- results_genes_unique_old1 %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(SYMBOL)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) #' How many Probes mapping to more than 1 SYMBOL
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>

Using Biomart adnotation from Ensembl GRCm39 ver 114. (28.05.2025) Loading Biomart adnotation

annot_new <- read.table("../mart_export_Final.txt", sep = "\t", header = TRUE, stringsAsFactors = FALSE)
annot_new$MGI_symbol <- NULL
str(annot_new)
## 'data.frame':    109541 obs. of  3 variables:
##  $ ENSEMBL: chr  "ENSMUSG00000064336" "ENSMUSG00000064336" "ENSMUSG00000064336" "ENSMUSG00000064337" ...
##  $ PROBEID: int  10598020 10598018 10598023 10598020 10598018 10598023 10598025 10598023 10598025 10598027 ...
##  $ SYMBOL : chr  "mt-Tf" "mt-Tf" "mt-Tf" "mt-Rnr1" ...
head(annot_new)
##              ENSEMBL  PROBEID  SYMBOL
## 1 ENSMUSG00000064336 10598020   mt-Tf
## 2 ENSMUSG00000064336 10598018   mt-Tf
## 3 ENSMUSG00000064336 10598023   mt-Tf
## 4 ENSMUSG00000064337 10598020 mt-Rnr1
## 5 ENSMUSG00000064337 10598018 mt-Rnr1
## 6 ENSMUSG00000064337 10598023 mt-Rnr1

Merging DE results with new annotation

results_annot_new <- merge(resultsF, annot_new, by.x = "row.names", by.y = "PROBEID")
head(results_annot_new)
##   Row.names       logFC        CI.L        CI.R   AveExpr          t    P.Value
## 1  10338074 -0.06667961 -0.27720381  0.14384459 12.130281 -0.6817806 0.50692211
## 2  10338075 -0.28691723 -0.52697809 -0.04685637  8.840208 -2.5726983 0.02264609
## 3  10338076  0.22366797 -0.07914274  0.52647868  9.355779  1.5899598 0.13501230
## 4  10338077 -0.13996187 -0.41329318  0.13336944 11.509166 -1.1022343 0.28964868
## 5  10338084  0.09433442 -0.27233280  0.46100165  8.002068  0.5537984 0.58878485
## 6  10338084  0.09433442 -0.27233280  0.46100165  8.002068  0.5537984 0.58878485
##   adj.P.Val         B            ENSEMBL  SYMBOL
## 1 0.7160388 -6.140468 ENSMUSG00000030967  Zranb1
## 2 0.1808699 -3.586456 ENSMUSG00000032112 Trappc4
## 3 0.3742799 -5.172681 ENSMUSG00000079477    Rab7
## 4 0.5354559 -5.772491 ENSMUSG00000020936    Nmt1
## 5 0.7714536 -6.220642 ENSMUSG00002075586 Gm54825
## 6 0.7714536 -6.220642 ENSMUSG00000071415   Rpl23

Adding ProbeId Column instead of rownames

colnames(results_annot_new)[1] <- "ProbeID"
str(results_annot_new)
## 'data.frame':    28621 obs. of  11 variables:
##  $ ProbeID  : chr  "10338074" "10338075" "10338076" "10338077" ...
##  $ logFC    : num  -0.0667 -0.2869 0.2237 -0.14 0.0943 ...
##  $ CI.L     : num  -0.2772 -0.527 -0.0791 -0.4133 -0.2723 ...
##  $ CI.R     : num  0.1438 -0.0469 0.5265 0.1334 0.461 ...
##  $ AveExpr  : num  12.13 8.84 9.36 11.51 8 ...
##  $ t        : num  -0.682 -2.573 1.59 -1.102 0.554 ...
##  $ P.Value  : num  0.5069 0.0226 0.135 0.2896 0.5888 ...
##  $ adj.P.Val: num  0.716 0.181 0.374 0.535 0.771 ...
##  $ B        : num  -6.14 -3.59 -5.17 -5.77 -6.22 ...
##  $ ENSEMBL  : chr  "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
##  $ SYMBOL   : chr  "Zranb1" "Trappc4" "Rab7" "Nmt1" ...

filtering out rows without SYMBOL or ENSEMBL

results_annot_new <- results_annot_new %>%
  filter(
    (!is.na(SYMBOL) & SYMBOL != "") |
      (!is.na(ENSEMBL) & ENSEMBL != "")
  )

str(results_annot_new)
## 'data.frame':    28621 obs. of  11 variables:
##  $ ProbeID  : chr  "10338074" "10338075" "10338076" "10338077" ...
##  $ logFC    : num  -0.0667 -0.2869 0.2237 -0.14 0.0943 ...
##  $ CI.L     : num  -0.2772 -0.527 -0.0791 -0.4133 -0.2723 ...
##  $ CI.R     : num  0.1438 -0.0469 0.5265 0.1334 0.461 ...
##  $ AveExpr  : num  12.13 8.84 9.36 11.51 8 ...
##  $ t        : num  -0.682 -2.573 1.59 -1.102 0.554 ...
##  $ P.Value  : num  0.5069 0.0226 0.135 0.2896 0.5888 ...
##  $ adj.P.Val: num  0.716 0.181 0.374 0.535 0.771 ...
##  $ B        : num  -6.14 -3.59 -5.17 -5.77 -6.22 ...
##  $ ENSEMBL  : chr  "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
##  $ SYMBOL   : chr  "Zranb1" "Trappc4" "Rab7" "Nmt1" ...
head(results_annot_new)
##    ProbeID       logFC        CI.L        CI.R   AveExpr          t    P.Value
## 1 10338074 -0.06667961 -0.27720381  0.14384459 12.130281 -0.6817806 0.50692211
## 2 10338075 -0.28691723 -0.52697809 -0.04685637  8.840208 -2.5726983 0.02264609
## 3 10338076  0.22366797 -0.07914274  0.52647868  9.355779  1.5899598 0.13501230
## 4 10338077 -0.13996187 -0.41329318  0.13336944 11.509166 -1.1022343 0.28964868
## 5 10338084  0.09433442 -0.27233280  0.46100165  8.002068  0.5537984 0.58878485
## 6 10338084  0.09433442 -0.27233280  0.46100165  8.002068  0.5537984 0.58878485
##   adj.P.Val         B            ENSEMBL  SYMBOL
## 1 0.7160388 -6.140468 ENSMUSG00000030967  Zranb1
## 2 0.1808699 -3.586456 ENSMUSG00000032112 Trappc4
## 3 0.3742799 -5.172681 ENSMUSG00000079477    Rab7
## 4 0.5354559 -5.772491 ENSMUSG00000020936    Nmt1
## 5 0.7714536 -6.220642 ENSMUSG00002075586 Gm54825
## 6 0.7714536 -6.220642 ENSMUSG00000071415   Rpl23
write.csv(results_annot_new, "results/tables/diff_expr_resultsF_newannot.csv", row.names = FALSE)

Checking uniquness of the Probes and Genes How many ENSEMBL with more than 1 Probe

symbol_probe_counts <- results_annot_new %>%
  group_by(ENSEMBL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)

nrow(symbol_probe_counts)  
## [1] 3103

How many SYMBOL with more than 1 Probe

symbol_probe_counts <- results_annot_new %>%
  group_by(SYMBOL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)

nrow(symbol_probe_counts)  
## [1] 2884

How many Probes mapping to more than 1 ENSEMBL

probe_symbol_counts <- results_annot_new %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(ENSEMBL)) %>%
  filter(n_symbols > 1)

nrow(probe_symbol_counts) 
## [1] 2571

How many Probes mapping to more than 1 SYMBOL

probe_symbol_counts <- results_annot_new %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(SYMBOL)) %>%
  filter(n_symbols > 1)

nrow(probe_symbol_counts) 
## [1] 2500

Solving problems with Non unique Genes and Probes List of ProbeIDs with more than one gene based on SYMBOL or ENSEMBL

conflict_ids <- results_annot_new %>%
  group_by(ProbeID) %>%
  filter(n_distinct(SYMBOL) > 1 | n_distinct(ENSEMBL) > 1) %>%
  pull(ProbeID) %>%
  unique()
length(conflict_ids)
## [1] 2571

Removal of ProbeIDs with nonunique Genes If ProbeID with just 1 row - stays If SYMBOLs with the same ENSEMBL have common core, randomly choose one row. Other way remove rows.

filtered_results_new <- results_annot_new %>%
  group_by(ProbeID) %>%
  group_modify(~ {
    subdf <- .x
    if (nrow(subdf) == 1) return(subdf)
    
    unique_symbols <- unique(subdf$SYMBOL)
    unique_symbols <- unique_symbols[!is.na(unique_symbols) & unique_symbols != ""]
    
    unique_ensembls <- unique(subdf$ENSEMBL)
    unique_ensembls <- unique_ensembls[!is.na(unique_ensembls) & unique_ensembls != ""]
    
    roots <- stringr::str_extract(unique_symbols, "^[A-Za-z]{3,}")
    roots <- na.omit(roots)
    
    common_root <- length(roots) > 0 && length(unique(roots)) == 1
    single_valid_ensembl <- length(unique_ensembls) == 1
    
    if (common_root && single_valid_ensembl) {
      return(subdf[sample(nrow(subdf), 1), ])
    } else {
      return(subdf[0, ])
    }
  }) %>%
  ungroup()

str(filtered_results_new)
## tibble [13,588 × 11] (S3: tbl_df/tbl/data.frame)
##  $ ProbeID  : chr [1:13588] "10338074" "10338075" "10338076" "10338077" ...
##  $ logFC    : num [1:13588] -0.0667 -0.2869 0.2237 -0.14 -0.3049 ...
##  $ CI.L     : num [1:13588] -0.2772 -0.527 -0.0791 -0.4133 -0.4948 ...
##  $ CI.R     : num [1:13588] 0.1438 -0.0469 0.5265 0.1334 -0.115 ...
##  $ AveExpr  : num [1:13588] 12.13 8.84 9.36 11.51 11.06 ...
##  $ t        : num [1:13588] -0.682 -2.573 1.59 -1.102 -3.456 ...
##  $ P.Value  : num [1:13588] 0.50692 0.02265 0.13501 0.28965 0.00406 ...
##  $ adj.P.Val: num [1:13588] 0.716 0.1809 0.3743 0.5355 0.0925 ...
##  $ B        : num [1:13588] -6.14 -3.59 -5.17 -5.77 -1.96 ...
##  $ ENSEMBL  : chr [1:13588] "ENSMUSG00000030967" "ENSMUSG00000032112" "ENSMUSG00000079477" "ENSMUSG00000020936" ...
##  $ SYMBOL   : chr [1:13588] "Zranb1" "Trappc4" "Rab7" "Nmt1" ...

Make pairs by SYMBOL

symbol_edges <- filtered_results_new %>%
  filter(!is.na(SYMBOL) & SYMBOL != "") %>%
  group_by(SYMBOL) %>%
  filter(n() > 1) %>%
  reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(symbol_edges)
## [1] 15112

Make pairs by ENSEMBL

ensembl_edges <- filtered_results_new %>%
  filter(!is.na(ENSEMBL) & ENSEMBL != "") %>%
  group_by(ENSEMBL) %>%
  filter(n() > 1) %>%
  reframe(pairs = combn(ProbeID, 2, simplify = FALSE))
nrow(ensembl_edges)
## [1] 15114

Connecting pairs lists

edges <- bind_rows(symbol_edges, ensembl_edges) %>%
  pull(pairs)
length(edges)
## [1] 30226

Making data.frame

edge_df <- do.call(rbind, lapply(edges, function(x) data.frame(from = x[1], to = x[2])))
str(edge_df)
## 'data.frame':    30226 obs. of  2 variables:
##  $ from: chr  "10519179" "10340510" "10340510" "10341744" ...
##  $ to  : chr  "10519181" "10341744" "10437263" "10437263" ...

Creating graph

g <- graph_from_data_frame(edge_df, directed = FALSE)
clusters <- components(g)

Annotatioing genes with clusters

cluster_map <- data.frame(ProbeID = names(clusters$membership),
                          gene_cluster = paste0("C", clusters$membership))

Joining clusters with z ProbeId, ENsembl, Symbol i DE

filtered_results_new_clustered <- filtered_results_new %>%
  left_join(cluster_map, by = "ProbeID") %>%
  mutate(gene_cluster = ifelse(is.na(gene_cluster), paste0("single_", ProbeID), gene_cluster))

Choose best ProbeiD by FDR or LogFC

results_genes_unique_new <- filtered_results_new_clustered %>%
  group_by(gene_cluster) %>%
  arrange(adj.P.Val, desc(abs(logFC))) %>%
  summarise(best_row = list(first(cur_data())), .groups = "drop") %>%
  unnest(best_row) %>%
  dplyr::select(-gene_cluster) %>%
  as.data.frame()

head(results_genes_unique_new)
##    ProbeID       logFC        CI.L       CI.R   AveExpr          t     P.Value
## 1 10519179  0.07262673 -0.14246846 0.28772191  9.801597  0.7268075 0.479774811
## 2 10554045  0.50220015  0.28834825 0.71605205  8.177063  5.0549552 0.000197222
## 3 10591622  0.28323591  0.08941603 0.47705579 10.042017  3.1456006 0.007442746
## 4 10364856  0.29456008  0.11274592 0.47637423 11.516333  3.4873841 0.003814862
## 5 10343405 -0.24754960 -0.51034389 0.01524469  9.726731 -2.0276822 0.062834560
## 6 10368068  0.21639148 -0.04646521 0.47924818  8.147441  1.7720449 0.098974580
##    adj.P.Val          B            ENSEMBL        SYMBOL
## 1 0.69551053 -6.1085740 ENSMUSG00000096221 1500002C15Rik
## 2 0.02246447  0.9415169 ENSMUSG00000058145      Adamts17
## 3 0.12106678 -2.5420019 ENSMUSG00000032198         Dock6
## 4 0.09103721 -1.9053815 ENSMUSG00000061589         Dot1l
## 5 0.26719623 -4.5135722 ENSMUSG00000026810          Dpm2
## 6 0.32626035 -4.9101970 ENSMUSG00000071392         Ect2l
str(results_genes_unique_new)
## 'data.frame':    11920 obs. of  11 variables:
##  $ ProbeID  : chr  "10519179" "10554045" "10591622" "10364856" ...
##  $ logFC    : num  0.0726 0.5022 0.2832 0.2946 -0.2475 ...
##  $ CI.L     : num  -0.1425 0.2883 0.0894 0.1127 -0.5103 ...
##  $ CI.R     : num  0.2877 0.7161 0.4771 0.4764 0.0152 ...
##  $ AveExpr  : num  9.8 8.18 10.04 11.52 9.73 ...
##  $ t        : num  0.727 5.055 3.146 3.487 -2.028 ...
##  $ P.Value  : num  0.479775 0.000197 0.007443 0.003815 0.062835 ...
##  $ adj.P.Val: num  0.6955 0.0225 0.1211 0.091 0.2672 ...
##  $ B        : num  -6.109 0.942 -2.542 -1.905 -4.514 ...
##  $ ENSEMBL  : chr  "ENSMUSG00000096221" "ENSMUSG00000058145" "ENSMUSG00000032198" "ENSMUSG00000061589" ...
##  $ SYMBOL   : chr  "1500002C15Rik" "Adamts17" "Dock6" "Dot1l" ...
write.csv(results_genes_unique_new, "results/tables/diff_expr_resultsF_new_annot_uniq.csv", row.names = FALSE)

Checking uniquness of Probes and Genes How many ENSEMBL with more than 1 Probe

symbol_probe_counts <- results_genes_unique_new %>%
  group_by(ENSEMBL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 0
symbol_probe_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ENSEMBL <chr>, n_probes <int>

How many SYMBOL with more than 1 Probe

symbol_probe_counts <- results_genes_unique_new %>%
  group_by(SYMBOL) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 1
symbol_probe_counts
## # A tibble: 1 × 2
##   SYMBOL n_probes
##   <chr>     <int>
## 1 ""           65

How many Probes mapping to more than 1 ENSEMBL

probe_symbol_counts <- results_genes_unique_new %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(ENSEMBL)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) 
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>

How many Probes mapping to more than 1 SYMBOL

probe_symbol_counts <- results_genes_unique_new %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(SYMBOL)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) 
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>

Merging DE tables with Oryginal and New annotation one set of statistics columns and annotations for both df1 - Oryginal and df2 - New annotations. genes from new Annotation: results_genes_unique_new GENES FROM Oryginal annotation: results_genes_unique_old1 Loading Oryginal and New annotations

df1 <- results_genes_unique_old1
df2 <- results_genes_unique_new

Extract statistics and annotations from df1 and df2 per ProbeID

df1_core <- df1 %>% dplyr::select(ProbeID, logFC, CI.L, CI.R, AveExpr, t, P.Value, adj.P.Val, B)
df1_annot <- df1 %>% dplyr::select(ProbeID, SYMBOL, ENSEMBL) %>%
  dplyr::rename(SYMBOL.df1 = SYMBOL, ENSEMBL.df1 = ENSEMBL)

df2_core <- df2 %>% dplyr::select(ProbeID, logFC, CI.L, CI.R, AveExpr, t, P.Value, adj.P.Val, B)
df2_annot <- df2 %>% dplyr::select(ProbeID, SYMBOL, ENSEMBL) %>%
  dplyr::rename(SYMBOL.df2 = SYMBOL, ENSEMBL.df2 = ENSEMBL)

Setting lists common and unique ProbeIds

common_ids <- intersect(df1$ProbeID, df2$ProbeID)
only_df1_ids <- setdiff(df1$ProbeID, df2$ProbeID)
only_df2_ids <- setdiff(df2$ProbeID, df1$ProbeID)

Making lists of common rows from df1 and df2 with same statistics and different annotations

common_core <- df1_core %>% filter(ProbeID %in% common_ids)
common_annot_df1 <- df1_annot %>% filter(ProbeID %in% common_ids)
common_annot_df2 <- df2_annot %>% filter(ProbeID %in% common_ids)

Making combined table with common Ids and diferential annotation

common_combined <- common_core %>%
  left_join(common_annot_df1, by = "ProbeID") %>%
  left_join(common_annot_df2, by = "ProbeID") %>%
  mutate(status = "common")
str(common_combined)
## 'data.frame':    10280 obs. of  14 variables:
##  $ ProbeID    : chr  "10394783" "10531181" "10587627" "10448559" ...
##  $ logFC      : num  0.4118 0.1685 0.0361 0.2136 -0.1938 ...
##  $ CI.L       : num  -0.0519 -0.0297 -0.1651 -0.0959 -0.4116 ...
##  $ CI.R       : num  0.875 0.367 0.237 0.523 0.024 ...
##  $ AveExpr    : num  9.46 8.06 10.22 7.93 8.95 ...
##  $ t          : num  1.912 1.83 0.386 1.486 -1.915 ...
##  $ P.Value    : num  0.0774 0.0894 0.7052 0.1604 0.0769 ...
##  $ adj.P.Val  : num  0.292 0.312 0.848 0.401 0.291 ...
##  $ B          : num  -4.7 -4.82 -6.3 -5.31 -4.69 ...
##  $ SYMBOL.df1 : chr  "1700030C10Rik" "Adamts3" "Cyb5r4" "D330041H03Rik" ...
##  $ ENSEMBL.df1: chr  "ENSMUSG00000099759" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000073437" ...
##  $ SYMBOL.df2 : chr  "Gm49327" "Adamts3" "Cyb5r4" "D330041H03Rik" ...
##  $ ENSEMBL.df2: chr  "ENSMUSG00000121309" "ENSMUSG00000043635" "ENSMUSG00000032872" "ENSMUSG00000073437" ...
##  $ status     : chr  "common" "common" "common" "common" ...

Extracting df1 specific rows

unique_df1 <- df1_core %>%
  filter(ProbeID %in% only_df1_ids) %>%
  left_join(df1_annot, by = "ProbeID") %>%
  mutate(SYMBOL.df2 = NA, ENSEMBL.df2 = NA, status = "only_in_df1")

Extracting df2 specific rows

unique_df2 <- df2_core %>%
  filter(ProbeID %in% only_df2_ids) %>%
  left_join(df2_annot, by = "ProbeID") %>%
  mutate(SYMBOL.df1 = NA, ENSEMBL.df1 = NA, status = "only_in_df2")

Combine all rows

combined_all <- bind_rows(common_combined, unique_df1, unique_df2) %>%
  arrange(ProbeID)

str(combined_all)
## 'data.frame':    12747 obs. of  14 variables:
##  $ ProbeID    : chr  "10338120" "10338286" "10338294" "10338316" ...
##  $ logFC      : num  -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
##  $ CI.L       : num  -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
##  $ CI.R       : num  -0.156 0.324 0.236 0.614 0.162 ...
##  $ AveExpr    : num  9.73 11.91 9.29 8.49 9.18 ...
##  $ t          : num  -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
##  $ P.Value    : num  0.00434 0.1371 0.92576 0.04446 0.30562 ...
##  $ adj.P.Val  : num  0.0952 0.3759 0.9672 0.2339 0.5487 ...
##  $ B          : num  -2.03 -5.19 -6.37 -4.2 -5.81 ...
##  $ SYMBOL.df1 : chr  NA NA NA NA ...
##  $ ENSEMBL.df1: chr  NA NA NA NA ...
##  $ SYMBOL.df2 : chr  "Psma1" "Eif5" "" "Dcdc2b" ...
##  $ ENSEMBL.df2: chr  "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
##  $ status     : chr  "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...
head(combined_all)
##    ProbeID       logFC         CI.L        CI.R   AveExpr           t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800  9.734361 -3.42154126
## 2 10338286  0.13698607 -0.049549813  0.32352196 11.909141  1.58076609
## 3 10338294 -0.01090092 -0.258063142  0.23626130  9.289402 -0.09493682
## 4 10338316  0.31124142  0.008905418  0.61357742  8.489829  2.21595590
## 5 10338366 -0.15879425 -0.479770947  0.16218244  9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
##       P.Value  adj.P.Val         B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254       <NA>        <NA>      Psma1
## 2 0.137100711 0.37587308 -5.185438       <NA>        <NA>       Eif5
## 3 0.925761643 0.96716779 -6.374166       <NA>        <NA>           
## 4 0.044460876 0.23393850 -4.203989       <NA>        <NA>     Dcdc2b
## 5 0.305616368 0.54867358 -5.811225       <NA>        <NA>    Gm47260
## 6 0.009104184 0.13010425 -2.732831       <NA>        <NA>      Psmc5
##          ENSEMBL.df2      status
## 1 ENSMUSG00000030751 only_in_df2
## 2 ENSMUSG00000021282 only_in_df2
## 3 ENSMUSG00000123626 only_in_df2
## 4 ENSMUSG00000078552 only_in_df2
## 5 ENSMUSG00000113328 only_in_df2
## 6 ENSMUSG00000020708 only_in_df2

common annotation table

common_only <- combined_all %>%
  filter(status == "common")
str(common_only)
## 'data.frame':    10280 obs. of  14 variables:
##  $ ProbeID    : chr  "10344633" "10344637" "10344658" "10344707" ...
##  $ logFC      : num  -0.0337 -0.0848 -0.0362 -0.2313 -0.0754 ...
##  $ CI.L       : num  -0.221 -0.275 -0.227 -0.416 -0.41 ...
##  $ CI.R       : num  0.1536 0.1052 0.1549 -0.0465 0.2592 ...
##  $ AveExpr    : num  11.36 11.12 12.33 9.78 9.89 ...
##  $ t          : num  -0.387 -0.961 -0.408 -2.695 -0.485 ...
##  $ P.Value    : num  0.7048 0.3536 0.6898 0.0179 0.6352 ...
##  $ adj.P.Val  : num  0.848 0.595 0.84 0.168 0.804 ...
##  $ B          : num  -6.3 -5.91 -6.29 -3.37 -6.26 ...
##  $ SYMBOL.df1 : chr  "Tcea1" "Atp6v1h" "Rb1cc1" "Pcmtd1" ...
##  $ ENSEMBL.df1: chr  "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" "ENSMUSG00000051285" ...
##  $ SYMBOL.df2 : chr  "Tcea1" "Atp6v1h" "Rb1cc1" "Pcmtd1" ...
##  $ ENSEMBL.df2: chr  "ENSMUSG00000033813" "ENSMUSG00000033793" "ENSMUSG00000025907" "ENSMUSG00000051285" ...
##  $ status     : chr  "common" "common" "common" "common" ...
head(common_only)
##    ProbeID       logFC       CI.L       CI.R   AveExpr          t    P.Value
## 1 10344633 -0.03365629 -0.2208716  0.1535590 11.362263 -0.3869711 0.70481722
## 2 10344637 -0.08481478 -0.2748344  0.1052049 11.123007 -0.9607860 0.35357609
## 3 10344658 -0.03621075 -0.2273545  0.1549330 12.333149 -0.4077848 0.68983356
## 4 10344707 -0.23134278 -0.4161381 -0.0465474  9.779085 -2.6947498 0.01790379
## 5 10344723 -0.07543749 -0.4100356  0.2591607  9.885885 -0.4853078 0.63524949
## 6 10344725  0.17728497 -0.1146897  0.4692596  8.536757  1.3070145 0.21306273
##   adj.P.Val         B SYMBOL.df1        ENSEMBL.df1 SYMBOL.df2
## 1 0.8480457 -6.301155      Tcea1 ENSMUSG00000033813      Tcea1
## 2 0.5947829 -5.913296    Atp6v1h ENSMUSG00000033793    Atp6v1h
## 3 0.8395928 -6.292624     Rb1cc1 ENSMUSG00000025907     Rb1cc1
## 4 0.1684237 -3.368097     Pcmtd1 ENSMUSG00000051285     Pcmtd1
## 5 0.8040888 -6.257034       Rrs1 ENSMUSG00000061024       Rrs1
## 6 0.4586216 -5.540863     Adhfe1 ENSMUSG00000025911     Adhfe1
##          ENSEMBL.df2 status
## 1 ENSMUSG00000033813 common
## 2 ENSMUSG00000033793 common
## 3 ENSMUSG00000025907 common
## 4 ENSMUSG00000051285 common
## 5 ENSMUSG00000061024 common
## 6 ENSMUSG00000025911 common

Orriginal annotation table

df1_only <- combined_all %>%
  filter(status == "only_in_df1")
str(df1_only)
## 'data.frame':    827 obs. of  14 variables:
##  $ ProbeID    : chr  "10344624" "10344719" "10344741" "10345228" ...
##  $ logFC      : num  -0.118 -0.0595 -0.1345 -0.0667 0.0968 ...
##  $ CI.L       : num  -0.2925 -0.2346 -0.3353 -0.2527 -0.0774 ...
##  $ CI.R       : num  0.0565 0.1155 0.0663 0.1193 0.271 ...
##  $ AveExpr    : num  12.08 9.02 11.89 8.94 8.34 ...
##  $ t          : num  -1.455 -0.732 -1.442 -0.772 1.196 ...
##  $ P.Value    : num  0.169 0.477 0.172 0.454 0.252 ...
##  $ adj.P.Val  : num  0.411 0.693 0.415 0.675 0.499 ...
##  $ B          : num  -5.35 -6.1 -5.37 -6.07 -5.67 ...
##  $ SYMBOL.df1 : chr  "Lypla1" "Gm35144" "Hnrnpa3" "1700001G17Rik" ...
##  $ ENSEMBL.df1: chr  "ENSMUSG00000025903" NA "ENSMUSG00000059005" "ENSMUSG00000103746" ...
##  $ SYMBOL.df2 : chr  NA NA NA NA ...
##  $ ENSEMBL.df2: chr  NA NA NA NA ...
##  $ status     : chr  "only_in_df1" "only_in_df1" "only_in_df1" "only_in_df1" ...
head(df1_only)
##    ProbeID       logFC        CI.L       CI.R   AveExpr          t   P.Value
## 1 10344624 -0.11796296 -0.29245601 0.05653009 12.078768 -1.4551948 0.1685031
## 2 10344719 -0.05951958 -0.23455063 0.11551147  9.022949 -0.7319786 0.4767145
## 3 10344741 -0.13447443 -0.33526945 0.06632059 11.890702 -1.4415854 0.1722436
## 4 10345228 -0.06668892 -0.25269667 0.11931882  8.940137 -0.7717493 0.4535790
## 5 10345411  0.09677839 -0.07739997 0.27095674  8.339542  1.1960182 0.2523021
## 6 10346109  0.04937092 -0.13691799 0.23565982 11.825134  0.5704765 0.5777395
##   adj.P.Val         B    SYMBOL.df1        ENSEMBL.df1 SYMBOL.df2 ENSEMBL.df2
## 1 0.4106491 -5.354516        Lypla1 ENSMUSG00000025903       <NA>        <NA>
## 2 0.6925333 -6.104790       Gm35144               <NA>       <NA>        <NA>
## 3 0.4145708 -5.372244       Hnrnpa3 ENSMUSG00000059005       <NA>        <NA>
## 4 0.6747091 -6.074869 1700001G17Rik ENSMUSG00000103746       <NA>        <NA>
## 5 0.4986995 -5.670328       Arhgef4 ENSMUSG00000037509       <NA>        <NA>
## 6 0.7644046 -6.211086        Dnah7b ENSMUSG00000041144       <NA>        <NA>
##        status
## 1 only_in_df1
## 2 only_in_df1
## 3 only_in_df1
## 4 only_in_df1
## 5 only_in_df1
## 6 only_in_df1

New annotation table

df2_only <- combined_all %>%
  filter(status == "only_in_df2")
str(df2_only)
## 'data.frame':    1640 obs. of  14 variables:
##  $ ProbeID    : chr  "10338120" "10338286" "10338294" "10338316" ...
##  $ logFC      : num  -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
##  $ CI.L       : num  -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
##  $ CI.R       : num  -0.156 0.324 0.236 0.614 0.162 ...
##  $ AveExpr    : num  9.73 11.91 9.29 8.49 9.18 ...
##  $ t          : num  -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
##  $ P.Value    : num  0.00434 0.1371 0.92576 0.04446 0.30562 ...
##  $ adj.P.Val  : num  0.0952 0.3759 0.9672 0.2339 0.5487 ...
##  $ B          : num  -2.03 -5.19 -6.37 -4.2 -5.81 ...
##  $ SYMBOL.df1 : chr  NA NA NA NA ...
##  $ ENSEMBL.df1: chr  NA NA NA NA ...
##  $ SYMBOL.df2 : chr  "Psma1" "Eif5" "" "Dcdc2b" ...
##  $ ENSEMBL.df2: chr  "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
##  $ status     : chr  "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...
head(df2_only)
##    ProbeID       logFC         CI.L        CI.R   AveExpr           t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800  9.734361 -3.42154126
## 2 10338286  0.13698607 -0.049549813  0.32352196 11.909141  1.58076609
## 3 10338294 -0.01090092 -0.258063142  0.23626130  9.289402 -0.09493682
## 4 10338316  0.31124142  0.008905418  0.61357742  8.489829  2.21595590
## 5 10338366 -0.15879425 -0.479770947  0.16218244  9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
##       P.Value  adj.P.Val         B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254       <NA>        <NA>      Psma1
## 2 0.137100711 0.37587308 -5.185438       <NA>        <NA>       Eif5
## 3 0.925761643 0.96716779 -6.374166       <NA>        <NA>           
## 4 0.044460876 0.23393850 -4.203989       <NA>        <NA>     Dcdc2b
## 5 0.305616368 0.54867358 -5.811225       <NA>        <NA>    Gm47260
## 6 0.009104184 0.13010425 -2.732831       <NA>        <NA>      Psmc5
##          ENSEMBL.df2      status
## 1 ENSMUSG00000030751 only_in_df2
## 2 ENSMUSG00000021282 only_in_df2
## 3 ENSMUSG00000123626 only_in_df2
## 4 ENSMUSG00000078552 only_in_df2
## 5 ENSMUSG00000113328 only_in_df2
## 6 ENSMUSG00000020708 only_in_df2

Working on to set the final SYMBOL/ENSEMBL, with rules: If a given row comes only from df1 or df2 (status == “only_in_df1” or “only_in_df2”), we take the data from the corresponding source. If status == “common” (i.e., data is present in both sources): We prefer values from df1, unless the value is NA or ““, in which case we take it from df2. Set final SYMBOL/ENSEMBL Create temporary GENES column being contacanation of SYMBOL_final and ENSEMBL_final

combined_final <- combined_all %>%
  mutate(
    SYMBOL_final = case_when(
      status == "only_in_df1" ~ SYMBOL.df1,
      status == "only_in_df2" ~ SYMBOL.df2,
      status == "common" & !is.na(SYMBOL.df1) & SYMBOL.df1 != "" ~ SYMBOL.df1,
      status == "common" & (is.na(SYMBOL.df1) | SYMBOL.df1 == "") ~ SYMBOL.df2
    ),
    ENSEMBL_final = case_when(
      status == "only_in_df1" ~ ENSEMBL.df1,
      status == "only_in_df2" ~ ENSEMBL.df2,
      status == "common" & !is.na(ENSEMBL.df1) & ENSEMBL.df1 != "" ~ ENSEMBL.df1,
      status == "common" & (is.na(ENSEMBL.df1) | ENSEMBL.df1 == "") ~ ENSEMBL.df2
    ),
    GENES = paste0(SYMBOL_final, "_", ENSEMBL_final)
  )
head(combined_final)
##    ProbeID       logFC         CI.L        CI.R   AveExpr           t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800  9.734361 -3.42154126
## 2 10338286  0.13698607 -0.049549813  0.32352196 11.909141  1.58076609
## 3 10338294 -0.01090092 -0.258063142  0.23626130  9.289402 -0.09493682
## 4 10338316  0.31124142  0.008905418  0.61357742  8.489829  2.21595590
## 5 10338366 -0.15879425 -0.479770947  0.16218244  9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
##       P.Value  adj.P.Val         B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254       <NA>        <NA>      Psma1
## 2 0.137100711 0.37587308 -5.185438       <NA>        <NA>       Eif5
## 3 0.925761643 0.96716779 -6.374166       <NA>        <NA>           
## 4 0.044460876 0.23393850 -4.203989       <NA>        <NA>     Dcdc2b
## 5 0.305616368 0.54867358 -5.811225       <NA>        <NA>    Gm47260
## 6 0.009104184 0.13010425 -2.732831       <NA>        <NA>      Psmc5
##          ENSEMBL.df2      status SYMBOL_final      ENSEMBL_final
## 1 ENSMUSG00000030751 only_in_df2        Psma1 ENSMUSG00000030751
## 2 ENSMUSG00000021282 only_in_df2         Eif5 ENSMUSG00000021282
## 3 ENSMUSG00000123626 only_in_df2              ENSMUSG00000123626
## 4 ENSMUSG00000078552 only_in_df2       Dcdc2b ENSMUSG00000078552
## 5 ENSMUSG00000113328 only_in_df2      Gm47260 ENSMUSG00000113328
## 6 ENSMUSG00000020708 only_in_df2        Psmc5 ENSMUSG00000020708
##                        GENES
## 1   Psma1_ENSMUSG00000030751
## 2    Eif5_ENSMUSG00000021282
## 3        _ENSMUSG00000123626
## 4  Dcdc2b_ENSMUSG00000078552
## 5 Gm47260_ENSMUSG00000113328
## 6   Psmc5_ENSMUSG00000020708

make additoional temporary columns with info about annotation

combined_final <- combined_final %>%
  mutate(
    has_symbol = !is.na(SYMBOL_final) & SYMBOL_final != "",
    has_ensembl = !is.na(ENSEMBL_final) & ENSEMBL_final != "",
    has_both = has_symbol & has_ensembl, 
    has_any = has_symbol | has_ensembl
  )
head(combined_final)
##    ProbeID       logFC         CI.L        CI.R   AveExpr           t
## 1 10338120 -0.42064003 -0.685272063 -0.15600800  9.734361 -3.42154126
## 2 10338286  0.13698607 -0.049549813  0.32352196 11.909141  1.58076609
## 3 10338294 -0.01090092 -0.258063142  0.23626130  9.289402 -0.09493682
## 4 10338316  0.31124142  0.008905418  0.61357742  8.489829  2.21595590
## 5 10338366 -0.15879425 -0.479770947  0.16218244  9.181339 -1.06491481
## 6 10338486 -0.27127064 -0.463191264 -0.07935003 10.227305 -3.04252920
##       P.Value  adj.P.Val         B SYMBOL.df1 ENSEMBL.df1 SYMBOL.df2
## 1 0.004338430 0.09523126 -2.028254       <NA>        <NA>      Psma1
## 2 0.137100711 0.37587308 -5.185438       <NA>        <NA>       Eif5
## 3 0.925761643 0.96716779 -6.374166       <NA>        <NA>           
## 4 0.044460876 0.23393850 -4.203989       <NA>        <NA>     Dcdc2b
## 5 0.305616368 0.54867358 -5.811225       <NA>        <NA>    Gm47260
## 6 0.009104184 0.13010425 -2.732831       <NA>        <NA>      Psmc5
##          ENSEMBL.df2      status SYMBOL_final      ENSEMBL_final
## 1 ENSMUSG00000030751 only_in_df2        Psma1 ENSMUSG00000030751
## 2 ENSMUSG00000021282 only_in_df2         Eif5 ENSMUSG00000021282
## 3 ENSMUSG00000123626 only_in_df2              ENSMUSG00000123626
## 4 ENSMUSG00000078552 only_in_df2       Dcdc2b ENSMUSG00000078552
## 5 ENSMUSG00000113328 only_in_df2      Gm47260 ENSMUSG00000113328
## 6 ENSMUSG00000020708 only_in_df2        Psmc5 ENSMUSG00000020708
##                        GENES has_symbol has_ensembl has_both has_any
## 1   Psma1_ENSMUSG00000030751       TRUE        TRUE     TRUE    TRUE
## 2    Eif5_ENSMUSG00000021282       TRUE        TRUE     TRUE    TRUE
## 3        _ENSMUSG00000123626      FALSE        TRUE    FALSE    TRUE
## 4  Dcdc2b_ENSMUSG00000078552       TRUE        TRUE     TRUE    TRUE
## 5 Gm47260_ENSMUSG00000113328       TRUE        TRUE     TRUE    TRUE
## 6   Psmc5_ENSMUSG00000020708       TRUE        TRUE     TRUE    TRUE

Keep only best annotation per ProbeID (df1>common>hasboth>df1>common>df2)

combined_final <- combined_final %>%
  group_by(ProbeID) %>%
  arrange(
    desc(status == "only_in_df1" & has_both),       
    desc(status == "common" & has_both),            
    desc(status == "only_in_df1" & has_symbol),      
    desc(status == "common" & has_symbol),            
    desc(status == "only_in_df1" & has_any),       
    desc(status == "common" & has_any),            
    desc(has_both),                                 
    desc(has_symbol),
    desc(has_any),
    desc(status == "only_in_df1"),                 
    desc(status == "common")                        
  ) %>%
  slice(1) %>%
  ungroup()

Remove temporart columns

combined_final <- combined_final %>% dplyr::select(-SYMBOL.df1, -ENSEMBL.df1, -SYMBOL.df2, -ENSEMBL.df2, -has_symbol, -has_ensembl, -has_both, -has_any)
head(combined_final)
## # A tibble: 6 × 13
##   ProbeID    logFC     CI.L    CI.R AveExpr       t P.Value adj.P.Val     B
##   <chr>      <dbl>    <dbl>   <dbl>   <dbl>   <dbl>   <dbl>     <dbl> <dbl>
## 1 10338120 -0.421  -0.685   -0.156     9.73 -3.42   0.00434    0.0952 -2.03
## 2 10338286  0.137  -0.0495   0.324    11.9   1.58   0.137      0.376  -5.19
## 3 10338294 -0.0109 -0.258    0.236     9.29 -0.0949 0.926      0.967  -6.37
## 4 10338316  0.311   0.00891  0.614     8.49  2.22   0.0445     0.234  -4.20
## 5 10338366 -0.159  -0.480    0.162     9.18 -1.06   0.306      0.549  -5.81
## 6 10338486 -0.271  -0.463   -0.0794   10.2  -3.04   0.00910    0.130  -2.73
## # ℹ 4 more variables: status <chr>, SYMBOL_final <chr>, ENSEMBL_final <chr>,
## #   GENES <chr>
str(combined_final)
## tibble [12,747 × 13] (S3: tbl_df/tbl/data.frame)
##  $ ProbeID      : chr [1:12747] "10338120" "10338286" "10338294" "10338316" ...
##  $ logFC        : num [1:12747] -0.4206 0.137 -0.0109 0.3112 -0.1588 ...
##  $ CI.L         : num [1:12747] -0.68527 -0.04955 -0.25806 0.00891 -0.47977 ...
##  $ CI.R         : num [1:12747] -0.156 0.324 0.236 0.614 0.162 ...
##  $ AveExpr      : num [1:12747] 9.73 11.91 9.29 8.49 9.18 ...
##  $ t            : num [1:12747] -3.4215 1.5808 -0.0949 2.216 -1.0649 ...
##  $ P.Value      : num [1:12747] 0.00434 0.1371 0.92576 0.04446 0.30562 ...
##  $ adj.P.Val    : num [1:12747] 0.0952 0.3759 0.9672 0.2339 0.5487 ...
##  $ B            : num [1:12747] -2.03 -5.19 -6.37 -4.2 -5.81 ...
##  $ status       : chr [1:12747] "only_in_df2" "only_in_df2" "only_in_df2" "only_in_df2" ...
##  $ SYMBOL_final : chr [1:12747] "Psma1" "Eif5" "" "Dcdc2b" ...
##  $ ENSEMBL_final: chr [1:12747] "ENSMUSG00000030751" "ENSMUSG00000021282" "ENSMUSG00000123626" "ENSMUSG00000078552" ...
##  $ GENES        : chr [1:12747] "Psma1_ENSMUSG00000030751" "Eif5_ENSMUSG00000021282" "_ENSMUSG00000123626" "Dcdc2b_ENSMUSG00000078552" ...

Creating relations ProbeID - SYMBOL, ProbeID - ENSEMBL

symbol_edges <- combined_final %>%
  filter(!is.na(SYMBOL_final) & SYMBOL_final != "") %>%
  dplyr::select(ProbeID, SYMBOL_final) %>%
  rename(gene = SYMBOL_final)

ensembl_edges <- combined_final %>%
  filter(!is.na(ENSEMBL_final) & ENSEMBL_final != "") %>%
  dplyr::select(ProbeID, ENSEMBL_final) %>%
  rename(gene = ENSEMBL_final)

edges <- bind_rows(symbol_edges, ensembl_edges)
g <- graph_from_data_frame(edges, directed = FALSE)
clusters <- components(g)

Binding clusters to PRobeID

probe_to_cluster <- data.frame(
  ProbeID = names(clusters$membership),
  gene_cluster = paste0("G", clusters$membership)
)

combined_clustered <- combined_final %>%
  left_join(probe_to_cluster, by = "ProbeID")

For each gene group choose one ProbeID df1 > common > df2 > FDR > logFC

final_combined_unique <- combined_clustered %>%
  group_by(gene_cluster) %>%
  arrange(desc(status == "only_in_df1"), desc(status == "common"),
          adj.P.Val, desc(abs(logFC))) %>%
  slice(1) %>%
  ungroup()

Removing gene_cluster column

final_combined_unique <- final_combined_unique %>% dplyr::select(-gene_cluster)

Result

final_combined_unique <- as.data.frame(final_combined_unique)
str(final_combined_unique)
## 'data.frame':    12585 obs. of  13 variables:
##  $ ProbeID      : chr  "10567072" "10338763" "10344115" "10365136" ...
##  $ logFC        : num  -0.183 -0.493 -0.145 -0.268 -0.102 ...
##  $ CI.L         : num  -0.454 -0.772 -0.607 -0.499 -0.369 ...
##  $ CI.R         : num  0.0879 -0.2145 0.3163 -0.0368 0.1643 ...
##  $ AveExpr      : num  10.07 7.84 8.84 9.48 9.41 ...
##  $ t            : num  -1.454 -3.809 -0.678 -2.495 -0.826 ...
##  $ P.Value      : num  0.16881 0.00204 0.50937 0.02626 0.42316 ...
##  $ adj.P.Val    : num  0.411 0.0693 0.718 0.1929 0.6498 ...
##  $ B            : num  -5.36 -1.31 -6.14 -3.72 -6.03 ...
##  $ status       : chr  "only_in_df1" "only_in_df2" "only_in_df2" "common" ...
##  $ SYMBOL_final : chr  "Psma1" "Sap30l" "Gm44187" "Tle5" ...
##  $ ENSEMBL_final: chr  "ENSMUSG00000030751" "ENSMUSG00000020519" "ENSMUSG00000108268" "ENSMUSG00000054452" ...
##  $ GENES        : chr  "Psma1_ENSMUSG00000030751" "Sap30l_ENSMUSG00000020519" "Gm44187_ENSMUSG00000108268" "Tle5_ENSMUSG00000054452" ...
head(final_combined_unique)
##    ProbeID       logFC       CI.L        CI.R   AveExpr          t    P.Value
## 1 10567072 -0.18296161 -0.4538130  0.08788977 10.071536 -1.4540606 0.16881217
## 2 10338763 -0.49329505 -0.7720810 -0.21450908  7.841442 -3.8088112 0.00204166
## 3 10344115 -0.14538961 -0.6071189  0.31633971  8.839705 -0.6777968 0.50936668
## 4 10365136 -0.26785458 -0.4989202 -0.03678894  9.475127 -2.4952686 0.02626201
## 5 10556246 -0.10233761 -0.3690169  0.16434163  9.413671 -0.8260373 0.42316102
## 6 10556266 -0.09187057 -0.2799978  0.09625666 11.422159 -1.0511830 0.31165275
##    adj.P.Val         B      status SYMBOL_final      ENSEMBL_final
## 1 0.41100995 -5.355998 only_in_df1        Psma1 ENSMUSG00000030751
## 2 0.06930072 -1.306324 only_in_df2       Sap30l ENSMUSG00000020519
## 3 0.71803512 -6.143198 only_in_df2      Gm44187 ENSMUSG00000108268
## 4 0.19288391 -3.723343      common         Tle5 ENSMUSG00000054452
## 5 0.64978436 -6.031703      common       Zfp143 ENSMUSG00000061079
## 6 0.55450067 -5.825196      common         Wee1 ENSMUSG00000031016
##                        GENES
## 1   Psma1_ENSMUSG00000030751
## 2  Sap30l_ENSMUSG00000020519
## 3 Gm44187_ENSMUSG00000108268
## 4    Tle5_ENSMUSG00000054452
## 5  Zfp143_ENSMUSG00000061079
## 6    Wee1_ENSMUSG00000031016

Final uniqueness check no of rows without ENSEMBL

sum(is.na(final_combined_unique$ENSEMBL_final) | final_combined_unique$ENSEMBL_final == "") 
## [1] 78

no of rows without SYMBOL

sum(is.na(final_combined_unique$SYMBOL_final) | final_combined_unique$SYMBOL_final == "")  
## [1] 51

duplicated ProbeID

any(duplicated(final_combined_unique$ProbeID))   
## [1] FALSE

duplicated ENSEMBNL

any(duplicated(final_combined_unique$ENSEMBL_final))   
## [1] TRUE

duplicated SYMBOL

any(duplicated(final_combined_unique$SYMBOL_final)) 
## [1] TRUE

Duplication check how many ENSEMBL with >1 Probe

symbol_probe_counts <- final_combined_unique %>%
  group_by(ENSEMBL_final) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 1
symbol_probe_counts
## # A tibble: 1 × 2
##   ENSEMBL_final n_probes
##   <chr>            <int>
## 1 <NA>                78

how many SYMBOL with >1 Probe

symbol_probe_counts <- final_combined_unique %>%
  group_by(SYMBOL_final) %>%
  summarise(n_probes = n_distinct(ProbeID)) %>%
  filter(n_probes > 1)
nrow(symbol_probe_counts)  
## [1] 1
symbol_probe_counts
## # A tibble: 1 × 2
##   SYMBOL_final n_probes
##   <chr>           <int>
## 1 ""                 51

how many PROBES for more than 1 gene

probe_symbol_counts <- final_combined_unique %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(ENSEMBL_final)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) 
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>

how many PROBES for more than 1 gene

probe_symbol_counts <- final_combined_unique %>%
  group_by(ProbeID) %>%
  summarise(n_symbols = n_distinct(SYMBOL_final)) %>%
  filter(n_symbols > 1)
nrow(probe_symbol_counts) 
## [1] 0
probe_symbol_counts
## # A tibble: 0 × 2
## # ℹ 2 variables: ProbeID <chr>, n_symbols <int>
write.csv(final_combined_unique, "results/tables/final_combined_unique.csv", row.names = FALSE)

MA Plot

plotMA(fitF, coef = 2, main = "MA plot: KO6 vs KO5", ylim = c(-4, 4))

Volcano Plot FDR < 0.05 & abs(logFC) > 0.5

final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
  geom_point(aes(color = threshold)) +
  geom_text_repel(data = subset(final_combined_unique, threshold),
                  aes(label = SYMBOL_final), max.overlaps = 10) +
  scale_color_manual(values = c("grey", "red")) +
  geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
  theme_minimal() +
  labs(title = "Volcano plot: KO6 vs KO5")
ala
## Warning: ggrepel: 122 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
  geom_point(aes(color = threshold)) +
  geom_text_repel(data = subset(final_combined_unique, threshold),
                  aes(label = ENSEMBL_final), max.overlaps = 10) +
  scale_color_manual(values = c("grey", "red")) +
  geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
  theme_minimal() +
  labs(title = "Volcano plot: KO6 vs KO5")
ala
## Warning: Removed 1 row containing missing values or values outside the scale range
## (`geom_text_repel()`).
## Warning: ggrepel: 126 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

final_combined_unique$threshold <- final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5
ala <- ggplot(final_combined_unique, aes(x = logFC, y = -log10(P.Value))) +
  geom_point(aes(color = threshold)) +
  geom_text_repel(data = subset(final_combined_unique, threshold),
                  aes(label = GENES), max.overlaps = 10) +
  scale_color_manual(values = c("grey", "red")) +
  geom_vline(xintercept = c(-1, -0.5, 0.5, 1), linetype = "dashed", color = "blue") +
  theme_minimal() +
  labs(title = "Volcano plot: KO6 vs KO5")
ala
## Warning: ggrepel: 130 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

P-value Histogram

hist(final_combined_unique$P.Value, breaks = 50, col = "gray", main = "Histogram p-value")

Heatmap of 100 genes with lowest FDR

top100 <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 100)
top_expr <- plier_gcbg_log_filtered[top100$ProbeID, ]
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(top_expr)
pheatmap(top_expr, scale = "row",
         annotation_col = annotation_col,
         show_rownames = FALSE,
         main = "Heatmapa top 100 genów różnicowych")

Heatmap with 500 genes with lowest FDR

top500 <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 500)
top_expr <- plier_gcbg_log_filtered[top500$ProbeID, ]
annotation_col <- data.frame(Group = group)
rownames(annotation_col) <- colnames(top_expr)
pheatmap(top_expr, scale = "row",
         annotation_col = annotation_col,
         show_rownames = FALSE,
         main = "Heatmapa top 500 genów różnicowych")

Confidence intervals for log fold change (logFC): For each gene, we calculated the 95% confidence interval (CI) for the estimated log fold change using standard error and the appropriate quantile of the t-distribution. The interval provides a range within which the true logFC is expected to lie with 95% confidence. If the CI includes zero, the change in expression is not considered statistically significant. Narrow intervals indicate precise estimates, while wider intervals reflect greater variability in the data. CI Table (Confidence Interval)

final_combined_unique$Exclude_bio_change <- with(final_combined_unique, CI.L > -0.5 & CI.R < 0.5)
excluded <- final_combined_unique[final_combined_unique$Exclude_bio_change == TRUE, ]
write.csv(excluded, "results/tables/genes_excluded_biological_change_final_combined_unique.csv", row.names = FALSE)

CI Plot (Confidence Interval)

plotCI <- head(final_combined_unique[order(final_combined_unique$adj.P.Val), ], 50)
p_plotCI <- ggplot(plotCI, aes(x = reorder(GENES, logFC), y = logFC)) +
  geom_point() +
  geom_errorbar(aes(ymin = CI.L, ymax = CI.R), width = 0.2) +
  geom_hline(yintercept = c(-0.5, -1.0, 0.5, 1.0), linetype = "dashed", color = "red") +
  coord_flip() +
  theme_minimal() +
  labs(title = "LogFC ± CI (top 50)", y = "logFC", x = "Gen")
print(p_plotCI)

Enrichment Analyses List of DE Genes needed by TopGo and gProfiler

de_genes <- final_combined_unique$SYMBOL_final[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$SYMBOL_final) & final_combined_unique$SYMBOL_final != ""]
str(de_genes)
##  chr [1:135] "Gdpd3" "Shisa7" "Pop4" "Folh1" "Star" "AI429214" "Slc7a2" ...
length(de_genes)
## [1] 135
de_genesE <- final_combined_unique$ENSEMBL_final[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$ENSEMBL_final) & final_combined_unique$ENSEMBL_final != ""]
str(de_genesE)
##  chr [1:136] "ENSMUSG00000030703" "ENSMUSG00000053550" "ENSMUSG00000030423" ...
length(de_genesE)
## [1] 136
de_genesG <- final_combined_unique$GENES[final_combined_unique$adj.P.Val < 0.05 & abs(final_combined_unique$logFC) > 0.5 & !is.na(final_combined_unique$GENES) & final_combined_unique$GENES != ""]
str(de_genesE)
##  chr [1:136] "ENSMUSG00000030703" "ENSMUSG00000053550" "ENSMUSG00000030423" ...
length(de_genesE)
## [1] 136

FGSEA analysis (GSEA)

categories <- c("BP", "CC", "MF")

gene_ranks <- final_combined_unique$t
names(gene_ranks) <- final_combined_unique$SYMBOL_final[!is.na(final_combined_unique$SYMBOL_final) & final_combined_unique$SYMBOL_final != ""]
length(final_combined_unique$SYMBOL_final[is.na(final_combined_unique$SYMBOL_final) | final_combined_unique$SYMBOL_final == ""])
## [1] 51
names(gene_ranks)
##     [1] "Psma1"          "Sap30l"         "Gm44187"        "Tle5"          
##     [5] "Zfp143"         "Wee1"           "Swap70"         "Gm9132"        
##     [9] "Mical2"         "Parva"          "Tead1"          "Bmal1"         
##    [13] "Far1"           "Spon1"          "Tle2"           "Insc"          
##    [17] "1110004F10Rik"  "Gm44777"        "Nucb2"          "Tmc5"          
##    [21] "Ccp110"         "Vps35l"         "Iqck"           "Acsm2"         
##    [25] "Rexo5"          "Ankrd24"        "Ldaf1"          "Anks4b"        
##    [29] "Abca14"         "Abca15"         "Abca16"         "Gm32916"       
##    [33] "E130201H02Rik"  "Eef2k"          "Polr3e"         "Mfsd13b"       
##    [37] "Gm8290"         "Mettl9"         "Hs3st2"         "Ubfd1"         
##    [41] "Dctn5"          "Chp2"           "Rbbp6"          "Gm20274"       
##    [45] "Tnrc6a"         "Aqp8"           "Hs3st4"         "Zfp873"        
##    [49] "4930571K23Rik"  "Il4ra"          "Katnip"         "Sbk1"          
##    [53] "Rabep2"         "Tufm"           "Apobr"          "Sgf29"         
##    [57] "Bola2"          "Gdpd3"          "Gm4924"         "Ypel3"         
##    [61] "Doc2a"          "Hirip3"         "Kctd13"         "Sez6l2"        
##    [65] "Cdipt"          "AI467606"       "Fbrs"           "Rnf40"         
##    [69] "Ctf1"           "Txnrd1"         "Orai3"          "Setd1a"        
##    [73] "Hsd3b7"         "Bckdk"          "Kat8"           "Fus"           
##    [77] "Itgax"          "Itgad"          "Armc5"          "Slc5a2"        
##    [81] "1700028I16Rik"  "Bag3"           "Inpp5f"         "Plpp4"         
##    [85] "Wdr11"          "Gm23847"        "Plekha1"        "Htra1"         
##    [89] "Fam24a"         "Pstk"           "Acadsb"         "Taf10"         
##    [93] "Hmx3"           "Hmx2"           "Bub3"           "Gpr26"         
##    [97] "Gm10584"        "Lhpp"           "Bccip"          "Dock1"         
##   [101] "Nps"            "Foxi2"          "Washc4"         "Ptpre"         
##   [105] "Mgmt"           "Gm10578"        "Glrx3"          "Ppp2r2d"       
##   [109] "Dpysl4"         "Pwwp2b"         "Adgra1"         "Kndc1"         
##   [113] "Utf1"           "Rfk"            "Gm47247"        "Zfp511"        
##   [117] "Prap1"          "Mtg1"           "Or6f2"          "Scart2"        
##   [121] "Or13a19"        "Or13a18"        "Or13a28"        "Urah"          
##   [125] "Cimap1a"        "Gm5425"         "Psmd13"         "Gm15542"       
##   [129] "Nlrp6"          "Pgghg"          "Ifitm1"         "B4galnt4"      
##   [133] "Pkp3"           "Lrrc56"         "Phrf1"          "Drd4"          
##   [137] "4930463O16Rik"  "Tmem80"         "Taldo1"         "Rangrf"        
##   [141] "Snora52"        "Pnpla2"         "Tspan4"         "Muc5ac"        
##   [145] "Brsk2"          "Krtap5-3"       "Gm45889"        "Tcp11l2"       
##   [149] "Krtap5-4"       "Syt8"           "Tnni2"          "Lsp1"          
##   [153] "Tnnt3"          "Igf2os"         "Gm6471"         "Cd81"          
##   [157] "Kcnq1"          "Gm15580"        "Polr3b"         "Dhcr7"         
##   [161] "Acte1"          "Shank2"         "Gm10152"        "Fgf3"          
##   [165] "Fgf4"           "Fgf15"          "LTO1"           "Mrgprd"        
##   [169] "Zc3h3"          "Rfx4"           "Oscar"          "Tfpt"          
##   [173] "Tmc4"           "Mboat7"         "Pirb"           "Lair1"         
##   [177] "D030047H15Rik"  "Cdc42ep5"       "Gm5319"         "Rdh13"         
##   [181] "Ric8b"          "Ppp1r12c"       "Tnnt1"          "Tnni3"         
##   [185] "Dnaaf3"         "Syt5"           "Tmem86b"        "Ppp6r1"        
##   [189] "Hspbp1"         "Tmem150b"       "Cox6b2"         "Tmem263"       
##   [193] "Il11"           "Tmem238"        "Ube2s"          "Shisa7"        
##   [197] "Isoc2b"         "Zfp579"         "Zfp784"         "Rasl2-9"       
##   [201] "Zfp787"         "Zfp583"         "Psma5"          "Or6z6"         
##   [205] "Or10am5"        "Peg3"           "Zfp954"         "Gm45844"       
##   [209] "Clcn4"          "Aurkc"          "Zfp551"         "Zscan18"       
##   [213] "Zfp329"         "Pwp1"           "Zbtb45"         "Mzf1"          
##   [217] "Vmn1r86"        "Gm7965"         "Zswim9"         "Nlrp5-ps"      
##   [221] "Selenow"        "Nop53"          "Ehd2"           "Bicra"         
##   [225] "Abhd17a"        "Timp3"          "C5ar2"          "Ccdc9"         
##   [229] "Sae1"           "Npas1"          "Fkrp"           "Calm3"         
##   [233] "Ppp5c"          "Hif3a"          "Gm45150"        "Psg23"         
##   [237] "Gm5174"         "Qpctl"          "Gipr"           "Fosb"          
##   [241] "Polr1g"         "A930016O22Rik"  "Mark4"          "Bloc1s3"       
##   [245] "Ppp1r37"        "Gemin7"         "Clasrp"         "Tex18"         
##   [249] "Apoc4"          "Apoc1"          "Apoe"           "Bcam"          
##   [253] "Bcl3"           "Ceacam19"       "Pvr"            "Igsf23"        
##   [257] "Zfp109"         "Zfp61"          "1700113H08Rik"  "Zfp94"         
##   [261] "Tescl"          "Irgc"           "Pinlyp"         "Tex101"        
##   [265] "Lypd11"         "Cd177"          "Rabac1"         "Pou2f2"        
##   [269] "Erf"            "Igf1"           "Ceacam1"        "Cnfn"          
##   [273] "Cxcl17"         "Ceacam2"        "Erich4"         "Bckdha"        
##   [277] "Tmem91"         "Ccdc97"         "Axl"            "Cyp2s1"        
##   [281] "Nup37"          "Rpl37a"         "Mrpl41"         "Egln2"         
##   [285] "Rab4b"          "Mia"            "Snrpa"          "Itpkc"         
##   [289] "Ltbp4"          "Shkbp1"         "Sptbn4"         "Washc3"        
##   [293] "Pld3"           "Map3k10"        "Zfp974"         "Zfp780b"       
##   [297] "Zfp850"         "Psmc4"          "Selenov"        "Dll3"          
##   [301] "Timm50"         "Supt5"          "Gnptab"         "Plekhg2"       
##   [305] "Zfp36"          "Med29"          "Samd4b"         "Ifnl2"         
##   [309] "Pak4"           "Mrps12"         "Gm10648"        "Actn4"         
##   [313] "Eif3k"          "Sycp3"          "Ryr1"           "Spred3"        
##   [317] "Catsperg1"      "Kcnk6"          "2200002D01Rik"  "Spint2"        
##   [321] "Sipa1l3"        "Zfp940"         "Zfp566"         "Tbcb"          
##   [325] "Gm47081"        "Ovol3"          "Wdr62"          "Sdhaf1"        
##   [329] "Lrfn3"          "Gm25259"        "Hcst"           "Aplp1"         
##   [333] "Kirrel2"        "Proser3"        "Lin37"          "Arfgef1"       
##   [337] "Cdk17"          "Kmt2b"          "Zbtb32"         "Cox6b1"        
##   [341] "Etv2"           "Haus5"          "Pmis2"          "Tmem147"       
##   [345] "Ffar3"          "Cd22"           "Mag"            "Lta4h"         
##   [349] "Hamp2"          "Usf2"           "Lsr"            "Fxyd5"         
##   [353] "Fxyd1"          "Hpn"            "Scn1b"          "Gramd1a"       
##   [357] "Scgb2b23-ps"    "Scgb2b26"       "Ccdc38"         "Gm12760"       
##   [361] "Wtip"           "Uba2"           "Pdcd2l"         "Lsm14a"        
##   [365] "Chst8"          "Cebpg"          "Lrp3"           "Wdr88"         
##   [369] "Gpatch1"        "Gm3571"         "Faap24"         "Tdrd12"        
##   [373] "Nudt19"         "Rgs9bp"         "Pdcd5"          "Dpy19l3"       
##   [377] "Zfp507"         "Gm22302"        "Uri1"           "Pop4"          
##   [381] "Nr2c1"          "Gm5114"         "AI987944"       "Gm20449"       
##   [385] "Gm7224"         "4933421I07Rik"  "Gm54949"        "Zfp976"        
##   [389] "Zfp975"         "Rpl18a-ps4"     "Zfp715"         "Tmcc3"         
##   [393] "Iglon5"         "Siglecl2"       "Siglecl1"       "1700028J19Rik" 
##   [397] "Acp4"           "Gm18307"        "1700008O03Rik"  "Emc10"         
##   [401] "Zfp473"         "Atf5"           "Cep83"          "Tbc1d17"       
##   [405] "Ptov1"          "Med25"          "D7Bwg0826e"     "Cpt1c"         
##   [409] "Prmt1"          "Bcl2l12"        "Scaf1"          "Prr12"         
##   [413] "Fcgrt"          "Eea1"           "Rps11"          "Aldh16a1"      
##   [417] "Kash5"          "Cd37"           "Trpm4"          "Lin7b"         
##   [421] "Snrnp70"        "Dhdh"           "Nucb1"          "Fgf21"         
##   [425] "Dcn"            "Fut2"           "Sec1"           "Sphk2"         
##   [429] "Gm5897"         "Cyth2"          "Grin2d"         "Emp3"          
##   [433] "Kcnj11"         "Abcc8"          "Sergef"         "Epyc"          
##   [437] "Saal1"          "Hps5"           "Uevld"          "Gm45737"       
##   [441] "Ptpn5"          "Mrgpra3"        "Mrgprb3"        "Gm45086"       
##   [445] "E2f8"           "Dbx1"           "Acot11"         "Ccer1"         
##   [449] "Fancf"          "Svip"           "Gm9357"         "Gm6290"        
##   [453] "Nipa2"          "Gabra5"         "Gm6226"         "Snrpn"         
##   [457] "A230006K03Rik"  "Ube2nl"         "B530045E10Rik"  "Peg12"         
##   [461] "Chrna7"         "Klf13"          "Fan1"           "Mphosph10"     
##   [465] "Entrep2"        "Nsmce3"         "Aldh1a3"        "Asb7"          
##   [469] "Synm"           "Cep290"         "Gm7627"         "Nr2f2"         
##   [473] "Gm7693"         "Gm5335"         "Chd2"           "A830073O21Rik" 
##   [477] "Gm10619"        "St8sia2"        "Mrpl46"         "Det1"          
##   [481] "Mgat4c"         "Mfge8"          "Polg"           "Rhcg"          
##   [485] "Kif7"           "Plin1"          "Mesp1"          "Ap3s2"         
##   [489] "Idh2"           "Cib1"           "Rccd1"          "Rassf9"        
##   [493] "Unc45a"         "Fes"            "Furin"          "Crtc3"         
##   [497] "Wdr73"          "Nmb"            "Sec11a"         "Rps17"         
##   [501] "Homer2"         "Hdgfl3"         "Gm25587"        "Bnc1"          
##   [505] "Saxo2"          "Il16"           "Cfap161"        "Arnt2"         
##   [509] "Fah"            "Zfand6"         "Folh1"          "Tmem135"       
##   [513] "Ccdc81"         "Ccdc59"         "Hikeshi"        "Eed"           
##   [517] "Btf3-ps5"       "Ccdc83"         "Tmem126a"       "Tmem126b"      
##   [521] "Ankrd42"        "4632427E13Rik"  "Gm5037"         "Gm22226"       
##   [525] "Ppfia2"         "Thrsp"          "Aamdc"          "Rsf1os2"       
##   [529] "Capn5"          "Omp"            "Acer3"          "Tsku"          
##   [533] "A630091E08Rik"  "Emsy"           "Uvrag"          "Pawr"          
##   [537] "Serpinh1"       "Rps3"           "Snord15b"       "Tpbgl"         
##   [541] "F730035P03Rik"  "Spcs2"          "Rnf169"         "Pold3"         
##   [545] "Gm10603"        "P2ry6"          "Gm23105"        "Inppl1"        
##   [549] "Folr1"          "Il18bp"         "Rnf121"         "Art5"          
##   [553] "Rhog"           "Or55b3"         "Or55b10"        "Trim21"        
##   [557] "Trim68"         "Vps26c"         "E2f7"           "Or52r1"        
##   [561] "Or51s1"         "Or51h7"         "Or51g2"         "Usp17ld"       
##   [565] "Or52s19"        "Or52a5"         "Dnajc19-ps"     "Or51a42"       
##   [569] "Or51a43"        "Csrp2"          "Ubqln5"         "Trim30a"       
##   [573] "Or52n4"         "Or52x1"         "Or52b2"         "Gm4972"        
##   [577] "Cavin3"         "Apbb1"          "Trim3"          "Arfip2"        
##   [581] "Rpl6"           "Gm22504"        "Rrp8"           "Tpp1"          
##   [585] "Mrpl17"         "Or2ag15"        "Or2ag18"        "5330417H12Rik" 
##   [589] "Cyb5r2"         "Ric3"           "Stk33"          "Osbpl8"        
##   [593] "Trim66"         "BC051019"       "Ascl3"          "Nrip3"         
##   [597] "Dennd5a"        "Tmem41b"        "Rnf141"         "Lyve1"         
##   [601] "Irag1"          "Dkk3"           "Bbs10"          "Rras2"         
##   [605] "Cyp2r1"         "Plekha7"        "Pik3c2a"        "Gm4366"        
##   [609] "Arl6ip1"        "Smg1"           "Itpripl2"       "Tmc7"          
##   [613] "Knop1"          "Nap1l1"         "Gprc5b"         "Gpr139"        
##   [617] "Umod"           "Pdilt"          "Thumpd1"        "Eri2"          
##   [621] "Dcun1d3"        "Dnah3"          "Crym"           "Pdzd9"         
##   [625] "Gm5176"         "Cdr2"           "Gm9905"         "Usp31"         
##   [629] "Cog7"           "Palb2"          "Ern2"           "Arhgap17"      
##   [633] "Zkscan2"        "4933440M02Rik"  "Nsmce1"         "Phlda1"        
##   [637] "Gtf3c1"         "Gsg1l"          "Lat"            "Spns1"         
##   [641] "Sh2b1"          "Il27"           "Nupr1"          "Sult1a1"       
##   [645] "Coro1a"         "Ppp4c"          "Krr1"           "Tmem219"       
##   [649] "Asphd1"         "Pagr1a"         "Maz"            "Kif22"         
##   [653] "Qprt"           "Spn"            "Cd2bp2"         "Gm4532"        
##   [657] "Dctpp1"         "Glipr1l1"       "Zfp768"         "Zfp747"        
##   [661] "Zfp764l1"       "Zfp764"         "Zfp689"         "1700008J07Rik" 
##   [665] "Zfp629"         "1700120K04Rik"  "Bcl7c"          "Ctf2"          
##   [669] "Lypla1"         "Glipr1l2"       "Gm53374"        "Stx1b"         
##   [673] "Zfp668"         "Prss53"         "Vkorc1"         "Prss36"        
##   [677] "Pycard"         "Yipf5"          "Cox6a2"         "Rusf1"         
##   [681] "Caps2"          "Gm4768"         "Nsmce4a"        "Cuzd1"         
##   [685] "Fam24b"         "2310057M21Rik"  "Gm16477"        "Oat"           
##   [689] "Eef1akmt2"      "Ctbp2"          "Tex36"          "Kcnc2"         
##   [693] "Dhx32"          "D7Ertd443e"     "Insyn2a"        "Mki67"         
##   [697] "9430038I01Rik"  "Tcerg1l"        "Mapk1ip1"       "Nkx6-2"        
##   [701] "Gm4974"         "Spef1l"         "Gm26596"        "Msx3"          
##   [705] "Caly"           "Echs1"          "Or6b13"         "Syce1"         
##   [709] "Zfp941"         "Ifitm3"         "Ifitm6"         "Rnh1"          
##   [713] "Hras"           "Gm15723"        "Lmntd2"         "Mir210"        
##   [717] "Sct"            "Cend1"          "Slc25a22"       "Pidd1"         
##   [721] "Gm10575"        "Chid1"          "Gm16982"        "Muc6"          
##   [725] "Zfc3h1"         "Mob2"           "Dusp8"          "Krtap5-2"      
##   [729] "Krtap5-24"      "Krtap5-1"       "Gm5054"         "Ctsd"          
##   [733] "Igf2"           "Mir483"         "Ins2"           "Tspan8"        
##   [737] "Gm7290"         "Ascl2"          "Phlda2"         "Nap1l4"        
##   [741] "Gm23297"        "Tnfrsf23"       "Mrgprg"         "Nadsyn1"       
##   [745] "Cttn"           "Ppfia1"         "Ptprb"          "Fadd"          
##   [749] "Ano1"           "Smim38"         "Tpcn2"          "Myadm"         
##   [753] "Cacng7"         "Arhgef18"       "Saxo5"          "Zfp358"        
##   [757] "Camsap3"        "Kcnmb4os2"      "Retn"           "Trappc5"       
##   [761] "Evi5l"          "Lrrc8e"         "Ccl25"          "Zfp958"        
##   [765] "Gm45224"        "Gpi1"           "Abhd13"         "Col4a2"        
##   [769] "5330438D12Rik"  "Naxd"           "Ing1"           "Arhgef7"       
##   [773] "Tex29"          "Sox1ot"         "Sox1"           "Spaca7"        
##   [777] "4931415C17Rik"  "Atp11a"         "Mcf2l"          "Tcea1"         
##   [781] "Mdm1"           "F7"             "Cul4a"          "Tmco3"         
##   [785] "Grk1"           "Tmem255b"       "Cdc16"          "Upf3a"         
##   [789] "Champ1"         "Fbxo25"         "Dlgap2"         "Grip1"         
##   [793] "Cln8"           "Arhgef10"       "Kbtbd11"        "Mcph1"         
##   [797] "Agpat5"         "Defb46"         "Gm16425"        "AY761185"      
##   [801] "Defa26"         "Defb35"         "Tmbim4"         "Ccdc70"        
##   [805] "Vps36"          "Thsd1"          "Tpte"           "Mrps31"        
##   [809] "Slc20a2"        "Plat"           "Ank1"           "Nkx6-3"        
##   [813] "Tm2d2"          "4921513I03Rik"  "D830025C05Rik"  "Lsm1"          
##   [817] "Star"           "Rnf170"         "Erlin2"         "Plpbp"         
##   [821] "Tex24"          "Dusp26"         "Tti2"           "Purg"          
##   [825] "Gns"            "Hmgb1-rs17"     "Tex15"          "Gtf2e2"        
##   [829] "Mboat4"         "Saraf"          "Dusp4"          "Ppp1r3b"       
##   [833] "Rps12"          "Trmt9b"         "AI429214"       "D930020B18Rik" 
##   [837] "Tusc3"          "Micu3"          "Zdhhc2"         "Vps37a"        
##   [841] "Adam24"         "Adam25"         "Adam20"         "Adam39"        
##   [845] "Slc7a2"         "Gm6180"         "Kics2"          "Triml2"        
##   [849] "Gm2221"         "Fat1"           "Mtnr1a"         "Sorbs2"        
##   [853] "Pdlim3"         "Ccdc110"        "Cfap97"         "Cenpu"         
##   [857] "Irf2"           "Gm9081"         "Rwdd4a"         "AA386476"      
##   [861] "E030037K01Rik"  "4930555F03Rik"  "Aga"            "Asb5"          
##   [865] "Spata4"         "Gm47612"        "Hpgd"           "Fbxo8"         
##   [869] "Avpr1a"         "Hmgb2"          "Mfap3l"         "Hpf1"          
##   [873] "B230317F23Rik"  "Sh3rf1"         "Cbr4"           "Ddx60"         
##   [877] "Tmem192"        "Marchf1"        "Gm26123"        "Gm9102"        
##   [881] "Naf1"           "Sh2d4a"         "Atp6v1b2"       "Zfp930"        
##   [885] "Zfp781a"        "Atp13a1"        "Lpar2"          "Pbx4"          
##   [889] "Tssk6"          "Sugp1"          "Atp6v1h"        "Mettl1"        
##   [893] "Tm6sf2"         "Mef2b"          "Tmem161a"       "Sugp2"         
##   [897] "Homer3"         "Cope"           "Comp"           "Fkbp8"         
##   [901] "Ell"            "Isyna1"         "Cdk4"           "Lsm4"          
##   [905] "Jund"           "Iqcn"           "Pde4c"          "Il12rb1"       
##   [909] "A230052G05Rik"  "Myo9b"          "Use1"           "Ocel1"         
##   [913] "Babam1"         "B4galnt1"       "Ankle1"         "Dda1"          
##   [917] "Gtpbp3"         "Mvb12a"         "Slc27a1"        "Pgls"          
##   [921] "Niban3"         "Colgalt1"       "Jak3"           "Gm45756"       
##   [925] "Dctn2"          "Zfp882"         "Zfp617"         "Zfp961"        
##   [929] "Tpm4"           "Hsh2d"          "Fam32a"         "Ap1m1"         
##   [933] "Klf2"           "1700030K09Rik"  "Atp5mk"         "Ddit3"         
##   [937] "Sin3b"          "F2rl3"          "Hmgxb4"         "Tom1"          
##   [941] "Hmox1"          "Mcm5"           "Rasd2"          "Iqcm"          
##   [945] "0610038B21Rik"  "Slc10a7"        "Stac3"          "Otud4"         
##   [949] "Anapc10"        "Gm31223"        "Inpp4b"         "Mgat4d"        
##   [953] "Clgn"           "Ndufb7"         "Dnajb1"         "Gipc1"         
##   [957] "Gm54868"        "Ndufa4l2"       "Adgrl1"         "Asf1b"         
##   [961] "Prkaca"         "1700067K01Rik"  "Brme1"          "Mir23a"        
##   [965] "Mir24-2"        "Cacna1a"        "Gadd45gip1"     "Farsa"         
##   [969] "Stat6"          "Syce2"          "Klf1"           "Dnase2a"       
##   [973] "Rtbdn"          "Prdx2"          "Hook2"          "Trir"          
##   [977] "Fbxw9"          "Wdr83os"        "Man2b1"         "Nemp1"         
##   [981] "Orc6"           "Gpt2"           "Phkb"           "Lonp2"         
##   [985] "Gm10638"        "Rps13"          "4933402J07Rik"  "9430002A10Rik" 
##   [989] "Tent4b"         "Nkd1"           "Myo1a"          "Rps6"          
##   [993] "Chd9"           "Fto"            "Irx6"           "Mmp2"          
##   [997] "Capns2"         "Ces5a"          "Gnao1"          "Ogfod1"        
##  [1001] "Mt4"            "Rb1cc1"         "Zbtb39"         "Mt3"           
##  [1005] "Nup93"          "Slc12a3"        "Nlrc5"          "Ccl22"         
##  [1009] "Cx3cl1"         "Ccl17"          "Coq9"           "Drc7"          
##  [1013] "Katnb1"         "Prim1"          "Spmip8"         "Ccdc113"       
##  [1017] "Gm5912"         "Gins3"          "A330008L17Rik"  "Impdh2"        
##  [1021] "Gm5742"         "Cdh5"           "Bean1"          "Cmtm3"         
##  [1025] "Ptges3"         "K230015D01Rik"  "Car7"           "Ces2a"         
##  [1029] "Gm45725"        "Ces3b"          "Cbfb"           "Phaf1"         
##  [1033] "Fbxl8"          "Hsf4"           "E2f4"           "Gls2"          
##  [1037] "Tmem208"        "Slc9a5"         "Hsd11b2"        "Ripor1"        
##  [1041] "Pard6a"         "4933405L10Rik"  "Thap11"         "Nutf2"         
##  [1045] "Edc4"           "Nrn1l"          "Mip"            "Pskh1"         
##  [1049] "Dus2"           "Nfatc3"         "Prmt7"          "Gm10629"       
##  [1053] "Cdh3"           "Tango6"         "Utp4"           "Sntb2"         
##  [1057] "Vps4a"          "Timeless"       "Nip7"           "Cyb5b"         
##  [1061] "Nfat5"          "Zfhx3"          "Pmfbp1"         "Txnl4b"        
##  [1065] "Pkd1l3"         "Zfp821"         "Ap1g1"          "Zfp612"        
##  [1069] "Stat2"          "Cmtr2"          "Hydin"          "Vac14"         
##  [1073] "Mtss2"          "Cog4"           "Aars1"          "Pdpr"          
##  [1077] "Gm55089"        "Znrf1"          "Zfp1"           "Pan2"          
##  [1081] "Terf2ip"        "Syce1l"         "Wwox"           "Dynlrb2"       
##  [1085] "Cenpn"          "Atmin"          "Cmip"           "Plcg2"         
##  [1089] "Cdh13"          "Hsbp1"          "Cnpy2"          "Necab2"        
##  [1093] "Dnaaf1"         "Adad2"          "Wfdc1"          "Klhl36"        
##  [1097] "Crispld2"       "Cox4i1"         "Irf8"           "Foxf1"         
##  [1101] "Foxc2"          "Cs"             "Jph3"           "BC048644"      
##  [1105] "Zfp469"         "Zfpm1"          "Zc3h18"         "Il17c"         
##  [1109] "9330133O14Rik"  "Trappc2l"       "Gm10612"        "Gm16378"       
##  [1113] "Lamtor5"        "Pcmtd1"         "Ankrd52"        "Cdh15"         
##  [1117] "Dpep1"          "Cdk10"          "Zfp276"         "Tcf25"         
##  [1121] "Mc1r"           "Tubb3"          "Afg3l1"         "Gas8"          
##  [1125] "Rhou"           "Rnf41"          "Rab4a"          "Gm9901"        
##  [1129] "Gm3889"         "Cog2"           "Arv1"           "Gm9172"        
##  [1133] "Trim67"         "Tsnax"          "Disc1"          "Map3k21"       
##  [1137] "Smarcc2"        "Kcnk1"          "Coa6"           "Nrp1"          
##  [1141] "Gm9204"         "Itgb1"          "Ccdc7b"         "Insr"          
##  [1145] "Pex11g"         "Xab2"           "Clec4g"         "Pmel"          
##  [1149] "Cd209a"         "Rprl3"          "Gm7381"         "Cd209d"        
##  [1153] "Ctxn1"          "Timm44"         "Elavl1"         "Shcbp1"        
##  [1157] "Gm9457"         "Arglu1"         "Pym1"           "Nalf1"         
##  [1161] "Lig4"           "Gm32429"        "Rps16-ps3"      "Irs2"          
##  [1165] "Col4a1"         "Cars2"          "Ankrd10"        "Spaca7b"       
##  [1169] "Gm45420"        "Dnajc14"        "Gm15348"        "Pcid2"         
##  [1173] "Grtp1"          "Dcun1d2"        "Gas6"           "1700029H14Rik" 
##  [1177] "Rasa3"          "Semp2l2a"       "Tdrp"           "Erich1"        
##  [1181] "Sarnp"          "BB014433"       "Gm15357"        "Defb33"        
##  [1185] "Defa39"         "Defb15"         "Atp7b"          "Ckap2"         
##  [1189] "Vdac3"          "Polb"           "Ap3m2"          "Cd63"          
##  [1193] "Mir3107"        "Gins4"          "Adam18"         "Adam9"         
##  [1197] "Htra4"          "Tacc1"          "Ash2l"          "Hgsnat"        
##  [1201] "Pomk"           "Fnta"           "Or10p21"        "Hook3"         
##  [1205] "Proscos"        "Brf2"           "Got1l1"         "Gm8096"        
##  [1209] "Unc5d"          "Mak16"          "Gm8168"         "Gm5117"        
##  [1213] "Nrg1"           "Or6c1b"         "Gtpbp10"        "1700104B16Rik" 
##  [1217] "Rbpms"          "Dctn6"          "Gm8254"         "Rpl31-ps23"    
##  [1221] "Eri1"           "Gm5787"         "Dlc1"           "Gm10683"       
##  [1225] "Gm35144"        "Or6c3"          "Mir383"         "Msr1"          
##  [1229] "Gm2033"         "Cnot7"          "Gm8423"         "Mtus1"         
##  [1233] "Asah1"          "Frg1"           "Zfp353-ps"      "Triml1"        
##  [1237] "Ctdsp2"         "Zfp42"          "Adam26b"        "Adam26a"       
##  [1241] "Adam34l"        "Gm5347"         "Gm9908"         "Cfap96"        
##  [1245] "Ankrd37"        "Slc25a4"        "Primpol"        "Gm3213"        
##  [1249] "Stox2"          "Trappc11"       "Rps16"          "Cdkn2aip"      
##  [1253] "Tenm3"          "Gm6463"         "Neil3"          "Adam29"        
##  [1257] "Cep44"          "Sap30"          "Gm10097"        "Gm6012"        
##  [1261] "Galnt7"         "Clcn3"          "Palld"          "Msmo1"         
##  [1265] "Klhl2"          "Tma16"          "Gm7639"         "Psd3"          
##  [1269] "Lzts1"          "Esr1"           "Gm7684"         "Gm10033"       
##  [1273] "Zfp868"         "Zfp869"         "Cilp2"          "Yjefn3"        
##  [1277] "Ndufa13"        "Gatad2a"        "Gm7730"         "Armc6"         
##  [1281] "Akap12"         "Ddx49"          "Upf1"           "Klhl26"        
##  [1285] "Rex1bd"         "Kxd1"           "Mpv17l2"        "Ifi30"         
##  [1289] "Pik3r2"         "Arrdc2"         "Ccdc124"        "Gm25515"       
##  [1293] "Slc5a5"         "Rpl18a"         "Nr2f6"          "Ushbp1"        
##  [1297] "Abhd8"          "Plvap"          "Bst2"           "Tmem221"       
##  [1301] "Nxnl1"          "Unc13a"         "Plekhg1"        "B3gnt3"        
##  [1305] "Gm18860"        "Cyp4f18"        "Eps15l1"        "Calr3"         
##  [1309] "Cherp"          "Large1"         "Crry-ps"        "Gm22509"       
##  [1313] "Tmem184c"       "Iyd"            "Pou4f2"         "1700011L22Rik" 
##  [1317] "Tpd52"          "Zc3h15"         "4930505O20Rik"  "Smarca5"       
##  [1321] "Gab1"           "Usp38"          "Gm4899"         "Zfp330"        
##  [1325] "Ppp1r14c"       "Gm10645"        "Elmod2"         "Scoc"          
##  [1329] "Tecr"           "Pkn1"           "Adgre5"         "Gm10644"       
##  [1333] "Misp3"          "Il27ra"         "Rln3"           "Rrs1"          
##  [1337] "Ginm1"          "C330011M18Rik"  "Dcaf15"         "Cc2d1a"        
##  [1341] "Mir181d"        "Mir181c"        "Zswim4"         "D8Ertd738e"    
##  [1345] "Yju2b"          "Dand5"          "Gcdh"           "Ust"           
##  [1349] "Rnaseh2a"       "Junb"           "Get3"           "Wdr83"         
##  [1353] "Vps35"          "4921524J17Rik"  "Neto2"          "Gm16167"       
##  [1357] "Siah1a"         "Sall1"          "Sash1"          "Gm6625"        
##  [1361] "Gm6658"         "Aktip"          "Rpgrip1l"       "Irx3"          
##  [1365] "Crnde"          "Ces1a"          "Ces1d"          "Nudt21"        
##  [1369] "Bbs2"           "Stxbp5"         "Pllp"           "Ciapin1"       
##  [1373] "Kifc3"          "Cngb1"          "Cfap20"         "Prss54"        
##  [1377] "Slc38a7"        "Gm7191"         "Cdh11"          "Gm10631"       
##  [1381] "Adgb"           "Tk2"            "Cmtm4"          "Nae1"          
##  [1385] "Tradd"          "Matcap1"        "Mir328"         "Tppp3"         
##  [1389] "Zdhhc1"         "Enkd1"          "Ranbp10"        "Grm1"          
##  [1393] "Ctrl"           "Cenpt"          "Lcat"           "Ddx28"         
##  [1397] "Esrp2"          "Cog8"           "Tmed6"          "Nob1"          
##  [1401] "Psmd7"          "Gm56822"        "Utrn"           "Gm1943"        
##  [1405] "Dhx38"          "Ist1"           "Atxn1l"         "Gm38523"       
##  [1409] "Glg1"           "Mlkl"           "Fa2h"           "Bcar1"         
##  [1413] "Cfdp1"          "Stx11"          "Tmem170"        "Chst5"         
##  [1417] "Adat1"          "Kars1"          "Maf"            "Cdyl2"         
##  [1421] "Cmc2"           "1700030J22Rik"  "Gcsh"           "Sdr42e1"       
##  [1425] "Zc2hc1b"        "Mphosph6"       "Gm45722"        "Mbtps1"        
##  [1429] "Hsdl1"          "Cotl1"          "Zdhhc7"         "Emc8"          
##  [1433] "Fbxo31"         "Zcchc14"        "Klhdc4"         "Ltv1"          
##  [1437] "Slc7a5"         "Trhr2"          "Mvd"            "Rnf166"        
##  [1441] "Piezo1"         "Aprt"           "Galns"          "Cbfa2t3"       
##  [1445] "Ankrd11"        "Chmp1a"         "Adhfe1"         "Phactr2"       
##  [1449] "Spata2l"        "Fanca"          "Dbndd1"         "n-R5s136"      
##  [1453] "Acta1"          "Abcb10"         "Taf5l"          "Pgbd5"         
##  [1457] "Agt"            "2310022B05Rik"  "Aig1"           "Ttc13"         
##  [1461] "Fam89a"         "Exoc8"          "Egln1"          "Sipa1l2"       
##  [1465] "Irf2bp2"        "Gm26397"        "Rbm34"          "Ccdc7a"        
##  [1469] "A530040E14Rik"  "Gje1"           "Alkbh8"         "Gm24918"       
##  [1473] "Cwf19l2"        "Gucy1a2"        "Gm5363"         "Kbtbd3"        
##  [1477] "Msantd4"        "Tfdp1"          "Pdgfd"          "Mmp12"         
##  [1481] "Heca"           "Mmp10"          "Gm19324"        "1700128F08Rik" 
##  [1485] "Gm29785"        "Cwc15"          "Vstm5"          "Taf1d"         
##  [1489] "Smco4"          "Gm5119"         "Slc36a4"        "Abracl"        
##  [1493] "Gm4977"         "Gm7680"         "Chordc1"        "Ubtfl1"        
##  [1497] "Or7g30"         "Zfp317"         "Gm7769"         "Zfp846"        
##  [1501] "Ubl5"           "Pin1"           "Ect2l"          "Rdh8"          
##  [1505] "Shfl"           "Ppan"           "Mrpl4"          "Icam1"         
##  [1509] "Icam5"          "1700084C06Rik"  "Pde4a"          "Atg4d"         
##  [1513] "Qtrt1"          "Hebp2"          "Dnm2"           "AB124611"      
##  [1517] "Carm1"          "Ldlr"           "Ccdc159"        "Plppr2"        
##  [1521] "Swsap1"         "Prkcsh"         "Gm6581"         "Pigyl"         
##  [1525] "Arfgef3"        "Zfp872"         "Zfp809"         "Gm10701"       
##  [1529] "Cypt4"          "Septin7"        "Eepd1"          "B3gat1"        
##  [1533] "Thyn1"          "Igsf9b"         "Spata19"        "Gm4922"        
##  [1537] "Zbtb44"         "Tpi-rs4"        "Arhgap32"       "Kirrel3"       
##  [1541] "4930581F22Rik"  "Srpra"          "Rpusd4"         "Cdon"          
##  [1545] "Pus3"           "Pate11"         "Tnfaip3"        "Acrv1"         
##  [1549] "Fez1"           "Tmem218"        "Hepacam"        "Msantd2"       
##  [1553] "Siae"           "Tpt1"           "Or8b8"          "Or8c18"        
##  [1557] "Or8c20"         "Hnrnpa3"        "Pex7"           "Or8b56"        
##  [1561] "Gm8543"         "Or10s1"         "Tmem225"        "Zfp202"        
##  [1565] "Clmp"           "Hspa8"          "Snord14e"       "Gm48565"       
##  [1569] "Bsx"            "4933406P04Rik"  "Mir100hg"       "Gm10690"       
##  [1573] "Nectin1"        "Usp2"           "Ccdc153"        "Gm10686"       
##  [1577] "Dpagt1"         "H2ax"           "Hyou1"          "Slc37a4"       
##  [1581] "Semp2l2b"       "Ift46"          "Gm39326"        "Mpzl2"         
##  [1585] "Fxyd6"          "Fxyd2"          "Dscaml1"        "Bace1"         
##  [1589] "Pcsk7"          "A830035O19Rik"  "Apoa1"          "Ube2q2"        
##  [1593] "Apoa4"          "Apoa5"          "Zpr1"           "Bud13"         
##  [1597] "Cadm1"          "Gm5617"         "Usp28"          "Zw10"          
##  [1601] "Tmprss5"        "Drd2"           "Eya4"           "Gm11149"       
##  [1605] "Pih1d2"         "Cryab"          "Alg9"           "Btg4"          
##  [1609] "Pou2af1"        "Gm32819"        "Gm8959"         "Arhgap20"      
##  [1613] "Rdx"            "Enpp1"          "Btf3-ps15"      "Exph5"         
##  [1617] "4930550C14Rik"  "Slc35f2"        "Sh2d7"          "Ireb2"         
##  [1621] "Chrna5"         "Fbxo22"         "Rcn2"           "Pstpip1"       
##  [1625] "Akap7"          "Hmg20a"         "Cspg4"          "Imp3"          
##  [1629] "Snupn"          "Man2c1"         "Gm5121"         "Fam219b"       
##  [1633] "Scamp2"         "Edc3"           "Sema7a"         "Gm8681"        
##  [1637] "Cyp11a1"        "1600029O15Rik"  "Stoml1"         "Gm10657"       
##  [1641] "Hcn4"           "Adpgk"          "Celf6"          "Parp6"         
##  [1645] "Myo9a"          "Larp6"          "L3mbtl3"        "1700036A12Rik" 
##  [1649] "Uaca"           "Anp32a"         "Itga11"         "Calml4"        
##  [1653] "Gm24526"        "Aagab"          "Snord16a"       "Snapc5"        
##  [1657] "Tipin"          "Gm5649"         "Megf11"         "Dennd4a"       
##  [1661] "Ints14"         "Igdcc3"         "Cilp"           "Clpx"          
##  [1665] "Pdcd7"          "Rasl12"         "Spg21"          "Rbpms2"        
##  [1669] "Vxn"            "Lama2"          "Oaz2"           "Ppib"          
##  [1673] "Ciao2a"         "Herc1"          "Rps27l"         "C2cd4b"        
##  [1677] "Vps13c"         "Rora"           "Ice2"           "Anxa2"         
##  [1681] "Gm54670"        "Gtf2a2"         "Myo1e"          "Sltm"          
##  [1685] "Gm10642"        "Adam10"         "Aldh1a2"        "Zfp280d"       
##  [1689] "Mns1"           "Rfx7"           "Nedd4"          "4930519F09Rik" 
##  [1693] "Pygo1"          "Dnaaf4"         "Ccpg1"          "Rab27a"        
##  [1697] "Gm16551"        "Onecut1"        "Atosa"          "Arpp19"        
##  [1701] "Gnb5"           "Leo1"           "Rnf146"         "Gclc"          
##  [1705] "Elovl5"         "Cilk1"          "Gsta4"          "Ddx43"         
##  [1709] "Mto1"           "Myo6"           "Irak1bp1"       "Sh3bgrl2"      
##  [1713] "Bckdhb"         "Cenpw"          "Gm26126"        "Gm25125"       
##  [1717] "Dop1a"          "Rwdd2a"         "Prss35"         "Ripply2"       
##  [1721] "Cyb5r4"         "D030062O11Rik"  "Nt5e"           "Zfp949"        
##  [1725] "Hint3"          "Gm24463"        "Rasgrf1"        "Ctsh"          
##  [1729] "Adamts7"        "Gm22866"        "Plscr1l1"       "Plod2"         
##  [1733] "Paqr9"          "Pcolce2"        "Gk5"            "Supt4a"        
##  [1737] "Tfdp2"          "Rpl7a-ps10"     "Nmnat3"         "Gm28530"       
##  [1741] "Rbp1"           "Copb2"          "Prr23a4"        "Foxl2"         
##  [1745] "Faim"           "Dbr1"           "Zup1"           "Dzip1l"        
##  [1749] "Stag1"          "9630041A04Rik"  "Anapc13"        "Slco2a1"       
##  [1753] "Rab6b"          "Topbp1"         "Gm5372"         "Acad11"        
##  [1757] "Mrpl3"          "Rwdd1"          "Twf2"           "Tlr9"          
##  [1761] "Poc1a"          "Dusp7"          "Abhd14b"        "Pcbp4"         
##  [1765] "Rrp9"           "Iqcf1"          "Iqcf5"          "Nprl2"         
##  [1769] "Nt5dc1"         "Zmynd10"        "Tusc2"          "Hyal2"         
##  [1773] "Naa80"          "Hyal3"          "Ifrd2"          "Gm57056"       
##  [1777] "Mon1a"          "Mst1r"          "Camkv"          "Mcmdc2"        
##  [1781] "Marcks"         "Traip"          "Gmppb"          "Mst1"          
##  [1785] "Nicn1"          "Amt"            "Rhoa"           "Gpx1"          
##  [1789] "1700102P08Rik"  "BC048562"       "Ccdc71"         "Gtf3c6"        
##  [1793] "Lamb2"          "Dalrd3"         "Prkar2a"        "Nckipsd"       
##  [1797] "Uqcrc1"         "Col7a1"         "Ucn2"           "Pfkfb4"        
##  [1801] "Shisa5"         "Nme6"           "Cdk19os"        "Cdc25a"        
##  [1805] "Map4"           "Cspg5"          "Ccdc12"         "Myl3"          
##  [1809] "Prss42"         "Prss45"         "Prss46"         "Prss50"        
##  [1813] "Lrrc2"          "Cdc40"          "1700061E17Rik"  "Lrrfip2"       
##  [1817] "Epm2aip1"       "Trank1"         "Ubp1"           "4930520O04Rik" 
##  [1821] "C130032M10Rik"  "Dync1li1"       "Cmtm6"          "Osbpl10"       
##  [1825] "Gpr6"           "Gm9487"         "Gadl1"          "Azi2"          
##  [1829] "Itga9"          "Vill"           "Dlec1"          "Acaa1a"        
##  [1833] "Acvr2b"         "Exog"           "Wdr48"          "Fig4"          
##  [1837] "Slc25a38"       "Mobp"           "Myrip"          "Eif1b"         
##  [1841] "Gm7229"         "Entpd3"         "Rpl14"          "Trak1"         
##  [1845] "1700048O20Rik"  "Snrk"           "Smpd2"          "Mir138-1"      
##  [1849] "Topaz1"         "Zkscan7"        "Zfp105"         "Kif15"         
##  [1853] "Tmem42"         "Limd1"          "4930433N12Rik"  "Gm5362"        
##  [1857] "Aasdhppt"       "Cep57l1"        "Gria4"          "Dync2h1"       
##  [1861] "Birc2"          "Birc3"          "Cfap300"        "Arhgap42"      
##  [1865] "Endod1"         "Amotl1"         "1700012B09Rik"  "Mif"           
##  [1869] "Armc2"          "Med17"          "Deup1"          "Fat3"          
##  [1873] "Naalad2"        "Zfp558"         "Muc16"          "Or1m1"         
##  [1877] "Uba52"          "Zfp26"          "Zfp426"         "Foxo3"         
##  [1881] "Zfp266"         "Fbxl12"         "Olfm2"          "Col5a3"        
##  [1885] "Eif3g"          "Dnmt1"          "S1pr2"          "Fdx2"          
##  [1889] "Cdc37"          "S1pr5"          "Cspp1"          "Mtres1"        
##  [1893] "Kri1"           "Cdkn2d"         "Mir199a-1"      "Spc24"         
##  [1897] "Kank2"          "Dock6"          "Gm45914"        "Epor"          
##  [1901] "Rgl3"           "Odad3"          "Qrsl1"          "Zfp653"        
##  [1905] "Ecsit"          "Zfp599"         "Zfp810"         "Anln"          
##  [1909] "Rp9"            "Gm55908"        "Dpy19l1"        "Dpy19l2"       
##  [1913] "Glb1l2"         "Lin28b"         "Acad8"          "Vps26b"        
##  [1917] "Jam3"           "Ntm"            "Gm29724"        "St14"          
##  [1921] "Aplp2"          "Tmem45b"        "Barx2"          "Dcps"          
##  [1925] "Grik2"          "Foxred1"        "Fam118b"        "Hyls1"         
##  [1929] "Gm6762"         "Gm3428"         "Chek1"          "Stt3a"         
##  [1933] "Pknox2"         "Slc37a2"        "Nrgn"           "Gprc6a"        
##  [1937] "Tbrg1"          "AW551984"       "Or10d5"         "Or10d5j"       
##  [1941] "Or10d5b"        "Gramd1b"        "Jhy"            "Crtam"         
##  [1945] "Ubash3b"        "Gm25401"        "4933411G06Rik"  "Sorl1"         
##  [1949] "Grik4"          "Oaf"            "Rnf26"          "Gm10687"       
##  [1953] "Nlrx1"          "Hinfp"          "C2cd2l"         "Hmbs"          
##  [1957] "Vps11"          "Gopc"           "Myl6"           "Cenatac"       
##  [1961] "Foxr1"          "Upk2"           "Gm47204"        "Phldb1"        
##  [1965] "Arcn1"          "Tmem25"         "Atp5mg"         "Cd3e"          
##  [1969] "Zfa-ps"         "Gm10684"        "Cep164"         "Gm7286"        
##  [1973] "Rnf214"         "Tagln"          "Pafah1b2"       "4931429L15Rik" 
##  [1977] "Gm10677"        "Nxpe2"          "Rexo2"          "Cep85l"        
##  [1981] "Nnmt"           "Htr3b"          "Ncam1"          "Pts"           
##  [1985] "Tex12"          "Sdhd"           "Nkapd1"         "Dlat"          
##  [1989] "Dixdc1"         "2310030G06Rik"  "Fam184a"        "Hspb2"         
##  [1993] "Sik2"           "Hoatz"          "Fdx1"           "Zc3h12c"       
##  [1997] "AI593442"       "Ddx10"          "Atm"            "Acat1"         
##  [2001] "Cul5"           "A830018L16Rik"  "Tbc1d32"        "Tnfaip8l3"     
##  [2005] "Cyp19a1"        "Gldnos"         "Dmxl2"          "Cib2"          
##  [2009] "Acsbg1"         "Skic8"          "Chrnb4"         "Etfa"          
##  [2013] "4930563M21Rik"  "Rps8"           "Tspan3"         "Peak1"         
##  [2017] "Cimap1c"        "Gm10658"        "Commd4"         "1700017B05Rik" 
##  [2021] "Ppcdc"          "Scamp5"         "Lman1l"         "Csk"           
##  [2025] "Edar"           "Ccdc33"         "Islr"           "Islr2"         
##  [2029] "Tbc1d21"        "Cd276"          "Neo1"           "Bbs4"          
##  [2033] "Tmem202"        "Senp8"          "Btf3-ps2"       "Oit3"          
##  [2037] "Nr2e3"          "Thsd4"          "Gm10655"        "Kif23"         
##  [2041] "Paqr5"          "Glce"           "Skor1"          "Map2k5"        
##  [2045] "2300009A05Rik"  "Smad6"          "Mcu"            "Dis3l"         
##  [2049] "Rab11a"         "Slc24a1"        "Hacd3"          "Ankdd1a"       
##  [2053] "Plekho2"        "Zfp609"         "Trip4"          "Snx1"          
##  [2057] "Usp3"           "Ddit4"          "Aph1b"          "Ppp1r2"        
##  [2061] "Aph1c"          "Rab8b"          "Lactb"          "Tpm1"          
##  [2065] "Tln2"           "M5C1000I18Rik"  "C2cd4a"         "Foxb1"         
##  [2069] "Anapc16"        "Gcnt3"          "Rnf111"         "Mindy2"        
##  [2073] "Lipc"           "Polr2m"         "Myzap"          "Cgnl1"         
##  [2077] "Tex9"           "Pigb"           "Unc13c"         "Cdh23"         
##  [2081] "Tmod3"          "Tmod2"          "Gm3671"         "Gm54715"       
##  [2085] "Mlip"           "Lrrc1"          "Fbxo9"          "Rn7sk"         
##  [2089] "Ooep"           "4930542C12Rik"  "Slc29a3"        "Slc17a5"       
##  [2093] "Col12a1"        "Cox7a2"         "Filip1"         "Htr1b"         
##  [2097] "Lca5"           "Tent5a"         "Gm22830"        "Ube3d"         
##  [2101] "Pgm3"           "Pldi"           "Cep162"         "Tbx18"         
##  [2105] "Slc25a40"       "Syncrip"        "Snhg5"          "Tmed3"         
##  [2109] "Tbc1d2b"        "Zic1"           "Dipk2a"         "Chst2"         
##  [2113] "Kcnb2"          "Sgpl1"          "Trpc1"          "Pls1"          
##  [2117] "1700065D16Rik"  "Nyx"            "Rasa2"          "E030011O05Rik" 
##  [2121] "Pxylp1"         "Spsb4"          "Clstn2"         "4930579K19Rik" 
##  [2125] "Adamts14"       "Mrps22"         "Gm5920"         "Foxl2os"       
##  [2129] "Gm1123"         "Pik3cb"         "Faiml"          "Mras"          
##  [2133] "Cldn18"         "Sox14"          "Il20rb"         "Pald1"         
##  [2137] "Nck1"           "Pccb"           "Ppp2r3a"        "Gm5161"        
##  [2141] "Ephb1"          "Cep63"          "Srprb"          "Trf"           
##  [2145] "Inhca"          "Tmem108"        "Eif4ebp2"       "Uba5"          
##  [2149] "Dnajc13"        "Acp3"           "Nudt16"         "Nudt16l2"      
##  [2153] "Atp2c1"         "Gm7436"         "Rpl10"          "Col6a6"        
##  [2157] "Col6a5"         "Macroh2a2"      "Col6a4"         "Ppm1m"         
##  [2161] "Alas1"          "Abhd14a"        "Gpr62"          "Iqcf3"         
##  [2165] "Iqcf4"          "Grm2"           "Tex264"         "Rbm15b"        
##  [2169] "Col13a1"        "Dock3"          "Mapkapk3"       "Hemk1"         
##  [2173] "Cyb561d2"       "Lsmem2"         "Sema3b"         "Sema3f"        
##  [2177] "Rbm6"           "Rnf123"         "Dag1"           "Fam241b"       
##  [2181] "Tcta"           "Klhdc8b"        "Wdr6"           "Gm7628"        
##  [2185] "Fbxw18"         "3000002C10Rik"  "Camp"           "Ptpn23"        
##  [2189] "Nradd"          "Nbeal2"         "Supv3l1"        "Pth1r"         
##  [2193] "Tmie"           "Rtp3"           "Mlh1"           "Mir128-2"      
##  [2197] "Pdcd6ip"        "Gm29825"        "Crtap"          "Trim71"        
##  [2201] "Cnot10"         "Vps26a"         "Gm7780"         "Gm5921"        
##  [2205] "Zcwpw2"         "Cmc1"           "Plcd1"          "Slc22a13"      
##  [2209] "Slc22a13b"      "Scn5a"          "Gorasp1"        "Csrnp1"        
##  [2213] "Srgn"           "Gm5922"         "Gm56077"        "Cck"           
##  [2217] "Lyzl4"          "Hhatl"          "Ccdc13"         "Pomgnt2"       
##  [2221] "Ano10"          "Gm26797"        "Zfp445"         "Itch"          
##  [2225] "Terf1"          "Ddx21"          "1110059G10Rik"  "Gm9856"        
##  [2229] "Tmem158"        "Slc6a20a"       "Lztfl1"         "Fyco1"         
##  [2233] "mt-Co2"         "mt-Tq"          "mt-Ts1"         "mt-Tp"         
##  [2237] "Ddx50"          "Tarm1"          "Maml2"          "Or10h1"        
##  [2241] "Taf1a"          "Dhrsx"          "Hhipl2"         "Tcstv7a"       
##  [2245] "A730008H23Rik"  "Brox"           "Disp1"          "Stox1"         
##  [2249] "Mia3"           "Ccl28"          "n-R5s2"         "Dgkk"          
##  [2253] "Gm14379"        "Foxp3"          "Syp"            "Gpkow"         
##  [2257] "Praf2"          "Smt3h2-ps"      "Hnrnph3"        "Tfe3"          
##  [2261] "Gripap1"        "Otud5"          "Pim2"           "Slc35a2"       
##  [2265] "Timm17b"        "Pcsk1n"         "Gm7079"         "Slc38a5"       
##  [2269] "4930402K13Rik"  "Mypn"           "Xk"             "H2ap"          
##  [2273] "H2al3"          "Sytl5"          "Mid1ip1"        "Atp6ap2"       
##  [2277] "AA414768"       "Cypt1"          "Maoa"           "Dusp21"        
##  [2281] "Reep3"          "Kdm6a"          "Rp2"            "Jade3"         
##  [2285] "Rbm10"          "Cdk16"          "Araf"           "Spaca5"        
##  [2289] "Gm5124"         "Gm9439"         "Slc6a14"        "Zfp365"        
##  [2293] "Ppp1r2-ps7"     "Wdr44"          "Tesl1"          "Dock11"        
##  [2297] "Il13ra1"        "Pgrmc1"         "Rpl7-ps9"       "Ube2a"         
##  [2301] "Rhox6"          "Rhox7a"         "Arid5b"         "Rhox13"        
##  [2305] "Zbtb33"         "Xiap"           "Stag2"          "Tex13c1"       
##  [2309] "Prr32"          "Actrt1"         "Ocrl"           "Utp14a"        
##  [2313] "Bcorl1"         "Cabcoco1"       "Slc25a14"       "Rbmx2"         
##  [2317] "Gm14719"        "Stk26"          "Ccdc160"        "Phf6"          
##  [2321] "Hprt1"          "Pabir3"         "Rtl8c"          "Ct55"          
##  [2325] "Cdk1"           "Smim10l2a"      "Ints6l"         "Slc9a6"        
##  [2329] "Brs3"           "Htatsf1"        "Vgll1"          "Magea13"       
##  [2333] "Gm715"          "Magec2"         "Magea9"         "Gm7634"        
##  [2337] "Gm47211"        "Ctag2"          "Fmr1"           "Fmr1nb"        
##  [2341] "Aff2"           "Gm16407"        "Gm8410"         "Mamld1"        
##  [2345] "Mtm1"           "Mtmr1"          "Vma21"          "Gm18636"       
##  [2349] "Nsdhl"          "Zfp185"         "Pnma3"          "F8a"           
##  [2353] "Bgn"            "Dusp9"          "Abcd1"          "Gm25226"       
##  [2357] "Ssr4"           "Gm23615"        "Bicc1"          "Avpr2"         
##  [2361] "Tktl1"          "Emd"            "Snora70"        "Tafazzin"      
##  [2365] "Atp6ap1"        "Fam50a"         "Gm6881"         "Gm15362"       
##  [2369] "Gm4989"         "Tfam"           "Dkc1"           "Brcc3"         
##  [2373] "Vbp1"           "Oat-rs1"        "Gm5397"         "Cldn34b4"      
##  [2377] "Tbl1x"          "4930480E11Rik"  "Gm8754"         "Fam47c"        
##  [2381] "Ube2d1"         "Gm8770"         "Tmem47"         "Fthl17a"       
##  [2385] "Tab3"           "Samt3"          "Nr0b1"          "Ppp4r3c-ps"    
##  [2389] "Gm6027"         "Gm14773"        "Gm5941"         "Cisd1"         
##  [2393] "Arx"            "Gm9009"         "Gspt2"          "Rpl13-ps5"     
##  [2397] "Pfn5"           "Msn"            "Gm9062"         "Ar"            
##  [2401] "Yipf6"          "Stard8"         "Gm4797"         "Efnb1"         
##  [2405] "Igbp1"          "Kif4"           "Gdpd2"          "Gm9078"        
##  [2409] "Med12"          "Nono"           "Taf1"           "Ogt"           
##  [2413] "Pin4"           "1700049L16Rik"  "Gm9109"         "Dmrtc1b"       
##  [2417] "Chic1"          "Tsx"            "Zcchc13"        "Pbdc1"         
##  [2421] "Cypt2"          "Fgf16"          "Tbx22"          "Tent5d"        
##  [2425] "Gm6419"         "Sh3bgrl"        "Cylc1"          "Tex16"         
##  [2429] "Zfp711"         "Ube2dnl1"       "Ube2dnl2"       "Gm5943"        
##  [2433] "Cpxcr1"         "Gm16373"        "Gm14926"        "Rsph14"        
##  [2437] "Pabpc5"         "Gm4993"         "Gm14942"        "Gm382"         
##  [2441] "4921511C20Rik"  "Mdm4-ps"        "Diaph2"         "Srpx2"         
##  [2445] "Arl13a"         "Tmem35a"        "Tmem70"         "Gucd1"         
##  [2449] "Cenpi"          "Gm16410"        "Rpl36a"         "Hnrnph2"       
##  [2453] "Pramex2"        "Bhlhb9"         "Arxes2"         "Tceal9"        
##  [2457] "Bex3"           "Nsa2-ps2"       "Lrrc75b"        "Tceal1"        
##  [2461] "BC065397"       "Zcchc18"        "Fam199x"        "Gm15043"       
##  [2465] "Nrk"            "4930513O06Rik"  "4933428M09Rik"  "Pwwp3b"        
##  [2469] "Radx"           "Susd2"          "Rnf128"         "Tbc1d8b"       
##  [2473] "Prps1"          "Mid2"           "Vsig1"          "Col4a5"        
##  [2477] "Nxt2"           "Gm7123"         "Gm15031"        "Tmem164"       
##  [2481] "Ddt"            "Pak3"           "Mir680-2"       "Trpc5os"       
##  [2485] "Mir448"         "Alas2"          "Pfkfb1"         "Fgd1"          
##  [2489] "Phf8"           "Gm15191"        "Hsd17b10"       "Gstt3"         
##  [2493] "Smc1a"          "Kdm5c"          "Ubqln2"         "Cypt3"         
##  [2497] "Amd-ps1"        "Acot9"          "Smpx"           "Klhl34"        
##  [2501] "Gm8659"         "Rps6ka3"        "Gstt1"          "Eif1ax"        
##  [2505] "Map7d2"         "Gm54697"        "Bclaf3"         "Sh3kbp1"       
##  [2509] "Gm8682"         "Phka2"          "Scml2"          "Gm15204"       
##  [2513] "Rbbp7"          "Gstt2"          "Gm16459"        "Ctps2"         
##  [2517] "Ap1s2"          "Pir"            "Vegfd"          "Piga"          
##  [2521] "Asb9"           "Gm8580"         "Gm7209"         "Gm15246"       
##  [2525] "Smarcb1"        "Mid1"           "Ezhip"          "Ccnb3"         
##  [2529] "Usp27x"         "2010204K13Rik"  "Ppp1r3f"        "Plp2"          
##  [2533] "Ccdc120"        "Pqbp1"          "Gata1"          "Mmp11"         
##  [2537] "Suv39h1"        "Wdr13"          "Tbc1d25"        "Ebp"           
##  [2541] "Ftsj1"          "Ssxb3"          "Dynlt3"         "Rpgr"          
##  [2545] "Gm14480"        "Gm14473"        "Slc5a4b"        "Gm14485"       
##  [2549] "1810030O07Rik"  "Med14"          "Cask"           "Ppp1r2-ps9"    
##  [2553] "Gm25207"        "Gm23516"        "Maob"           "Efhc2"         
##  [2557] "Fundc1"         "Gdap1"          "Prmt2"          "Tex13c3"       
##  [2561] "Ndufb11"        "Syn1"           "Cfp"            "Elk1"          
##  [2565] "Akap17b"        "Septin6"        "Rpl39"          "Upf3b"         
##  [2569] "Akap14"         "Pcnt"           "Ndufa1"         "Gm9"           
##  [2573] "Rhox1"          "Rhox8"          "Rhox9"          "Btg1c"         
##  [2577] "Tmem255a"       "Lamp2"          "Cul4b"          "C1galt1c1"     
##  [2581] "Col6a2"         "Gm7189"         "Gm5385"         "Gm14613"       
##  [2585] "Gm5135"         "Dcaf12l2"       "Dcaf12l1"       "Gm14652"       
##  [2589] "Gm4987"         "Smarca1"        "Apln"           "Col6a1"        
##  [2593] "Zdhhc9"         "Elf4"           "Aifm1"          "Zfp280c"       
##  [2597] "Enox2"          "Firre"          "Rap2c"          "Mbnl3"         
##  [2601] "Usp26"          "Magea14"        "Pcbp3"          "Gm6402"        
##  [2605] "Gm7851"         "Plac1"          "Pabir2"         "Mospd1"        
##  [2609] "AW822252"       "1700013H16Rik"  "Atf1-ps"        "Gm35586"       
##  [2613] "Gm773"          "Slx9"           "Ct45a"          "Mmgt1"         
##  [2617] "Map7d3"         "Arhgef6"        "Rbmx"           "Mir504"        
##  [2621] "Mcf2"           "Atp11c"         "Mir505"         "Gm4909"        
##  [2625] "Krtap12-24"     "Sox3"           "Sms"            "Gm14676"       
##  [2629] "4933436I01Rik"  "Ids"            "Gm14725"        "Gm14724"       
##  [2633] "Cd99l2"         "Gabre"          "Magea10"        "Lrrc3"         
##  [2637] "Haus7"          "Bcap31"         "Idh3g"          "Hcfc1"         
##  [2641] "Flna"           "Lage3"          "Gm44504"        "Fam3a"         
##  [2645] "G6pdx"          "Pls3"           "Pfkl"           "Prkx"          
##  [2649] "Prrg1"          "Gm8761"         "Gm5939"         "Cfap47"        
##  [2653] "Mageb16-ps1"    "Srsf19"         "Gk"             "Mageb4"        
##  [2657] "Gm5759"         "Aire"           "Dcaf8l"         "Fth1-ps"       
##  [2661] "Gm16465"        "Mageb18"        "Pdk3"           "Zfx"           
##  [2665] "Eif2s3x"        "Gm7061"         "Gm14830"        "Gm371"         
##  [2669] "Crispld1"       "Gatd3a"         "Asb12"          "Zc4h2"         
##  [2673] "1700010D01Rik"  "Las1l"          "Ophn1"          "Gm5760"        
##  [2677] "Pja1"           "P2ry4"          "Pdzd11"         "Gm14866"       
##  [2681] "Rrp1"           "Tex11"          "Snx12"          "Gm614"         
##  [2685] "Zmym3"          "Gm4779"         "Ercc6l"         "Cited1"        
##  [2689] "Phka1"          "1700031F05Rik"  "Dmrtc1a"        "Pdxk"          
##  [2693] "Cop1"           "Gm9785"         "Abcb7"          "Rpl12"         
##  [2697] "Atrx"           "Magt1"          "Fndc3c1"        "Itm2a"         
##  [2701] "Chmp1b2"        "Wmp"            "Tektl1"         "Gm379"         
##  [2705] "Brwd3"          "Hmgn5"          "Rps6ka6"        "Hdx"           
##  [2709] "Satl1"          "Chm"            "Gm5942"         "Gm14911"       
##  [2713] "Dmtf1l"         "2610008E11Rik"  "Cldn34c4"       "Gm7820"        
##  [2717] "Tspan6"         "Trmt2b"         "Taf7l"          "Gla"           
##  [2721] "Gm7855"         "Gm10344"        "Armcx2"         "Zmat1"         
##  [2725] "Plpp2"          "Tcp11x2"        "Tmsb15a"        "Nxf3"          
##  [2729] "Tceal8"         "Tceal5"         "Esx1"           "Gm8036"        
##  [2733] "Tex13a"         "Ripply1"        "Nup62cl"        "Mier2"         
##  [2737] "Tsc22d3"        "Psmd10"         "Acsl4"          "Gm4995"        
##  [2741] "Chrdl1"         "Capn6"          "Maged2"         "Gnl3l"         
##  [2745] "Tsr2"           "A230072E10Rik"  "C2cd4c"         "Gm4919"        
##  [2749] "Ribc1"          "Shroom2"        "Gm7150"         "Samt2b"        
##  [2753] "Cldn34b2"       "Gm4997"         "Sat1"           "Ptchd1"        
##  [2757] "Gm7312"         "Polrmt"         "Suclg2"         "Phex"          
##  [2761] "Gm15173"        "Gm8644"         "Cnksr2"         "Gm15190"       
##  [2765] "Pdha1"          "Ppef1"          "Cdkl5"          "Gja6"          
##  [2769] "Plppr3"         "Reps2"          "Txlng"          "Rnf138rt1"     
##  [2773] "Zrsr2"          "Car5b"          "Siah1b"         "Mospd2"        
##  [2777] "Ofd1"           "Rab9"           "Gm15229"        "Il17a"         
##  [2781] "Med16"          "Tmsb4x"         "Prps2"          "Gm6744"        
##  [2785] "Hccs"           "Vamp7"          "Uba1y"          "Kdm5d"         
##  [2789] "Eif2s3y"        "Uba1y-ps2"      "Zfy1"           "R3hdm4"        
##  [2793] "Uty"            "Ddx3y"          "Usp9y"          "Zfy2"          
##  [2797] "Sry"            "Gm28649"        "Srsy"           "4932431L22Rik" 
##  [2801] "Gm29276"        "Gm20826"        "Polr2e"         "Krt85"         
##  [2805] "Mrgpra4"        "Zfp1006"        "Dynll1"         "Rn18s-rs5"     
##  [2809] "Gm20939"        "Snrnp40"        "Noc2l"          "2310009B15Rik" 
##  [2813] "Fam90a1a"       "Sbno2"          "Ankrd63"        "Samd11"        
##  [2817] "Plekhn1"        "Ccdc82"         "Gm7073"         "Cbarp"         
##  [2821] "Gamt"           "2310011J03Rik"  "Pcsk4"          "Adamtsl5"      
##  [2825] "Mex3d"          "Paqr8"          "Uqcr11"         "Btbd2"         
##  [2829] "Mknk2"          "Plekhj1"        "Jsrp1"          "Lsm7"          
##  [2833] "Timm13"         "Lmnb2"          "Gng7"           "Diras1"        
##  [2837] "Efhc1"          "Slc39a3"        "Sgta"           "Mrpl54"        
##  [2841] "Tjp3"           "Gipc3"          "Hmg20b"         "Tektip1"       
##  [2845] "Fzr1"           "Nfic"           "Celf5"          "Gsta3"         
##  [2849] "Ncln"           "S1pr4"          "Gna11"          "Sirt6"         
##  [2853] "Zfp938"         "Spata31h1"      "Uqcc6"          "Glt8d2"        
##  [2857] "Nfyb"           "Slc41a2"        "B3gat2"         "Aldh1l2"       
##  [2861] "Ckap4"          "Mterf2"         "Cry1"           "Gm6714"        
##  [2865] "Prdm4"          "Rtcb"           "A230060F14Rik"  "Ascl1"         
##  [2869] "Parpbp"         "Rab7"           "Col9a1"         "Dram1"         
##  [2873] "Chpt1"          "Utp20"          "Gas2l3"         "Slc17a8"       
##  [2877] "Actr6"          "Apaf1"          "Slc25a3"        "Tmpo"          
##  [2881] "Cfap54"         "Lmbrd1"         "Snrpf"          "Vezt"          
##  [2885] "Cradd"          "Socs2"          "Mrpl42"         "Anapc15"       
##  [2889] "Gm20091"        "Gm8613"         "Csl"            "Tmtc3"         
##  [2893] "Gm19028"        "Rlig1"          "Alx1"           "Tmtc2"         
##  [2897] "Gm48298"        "Acss3"          "Myf5"           "Myf6"          
##  [2901] "Ptprq"          "Brcc3dc"        "Nav3"           "Dnaaf6rt"      
##  [2905] "Zdhhc17"        "Gm47866"        "Trhde"          "Gm55666"       
##  [2909] "Tbc1d15"        "Rab21"          "Thap2"          "Taf7l2"        
##  [2913] "Kcnmb4"         "Gm5781"         "Alyreffm2"      "Frs2"          
##  [2917] "Yeats4"         "Lyz2"           "Lyz1"           "Mdm2"          
##  [2921] "Nup107"         "Rap1b"          "Cdc5l"          "Dyrk2"         
##  [2925] "Irak3"          "1700001G17Rik"  "Rassf3"         "Tbk1"          
##  [2929] "Xpot"           "Srgap1"         "Rxylt1"         "Mirlet7i"      
##  [2933] "Atp23"          "Tsfm"           "Tspan31"        "Os9"           
##  [2937] "Rab23"          "Slc26a10"       "Arhgef25"       "Pip4k2c"       
##  [2941] "Kif5a"          "Mbd6"           "Mars1"          "Gli1"          
##  [2945] "Shmt2"          "Lrp1"           "Nab2"           "Dst"           
##  [2949] "Rbms2"          "Coq10a"         "Slc39a5"        "Nabp2"         
##  [2953] "Myl6b"          "Zc3h10"         "Pa2g4"          "Ikzf4"         
##  [2957] "Suox"           "Rpsa"           "Imp4"           "Ormdl2"        
##  [2961] "Or6c8b"         "Or6c8"          "Or6c201"        "Or10p1"        
##  [2965] "Or6c69b"        "Vmn2r86"        "Pisd-ps1"       "Eif4enif1"     
##  [2969] "Pla2g3"         "Cfc1"           "Selenom"        "Dusp18"        
##  [2973] "Pes1"           "Gal3st1"        "Gm11954"        "Sec14l4"       
##  [2977] "Sec14l3"        "Sf3a1"          "Castor1"        "Zmat5"         
##  [2981] "Canx"           "Arhgef4"        "Nipsnap1"       "Thoc5"         
##  [2985] "Ap1b1"          "Gm30172"        "Xbp1"           "Ankrd48"       
##  [2989] "Dbnl"           "Aebp1"          "Ykt6"           "Gm11401"       
##  [2993] "Plekhb2"        "Gm11971"        "Ccm2"           "Ramp3"         
##  [2997] "Adcy1"          "Gm11992"        "Gm11996"        "Spmip7"        
##  [3001] "Gm12009"        "Gm12011"        "Vstm2a"         "Hs6st1"        
##  [3005] "Akt2"           "Egfr"           "Ppp3r1"         "Dnaaf10"       
##  [3009] "Glul"           "Spred2"         "Rab1a"          "Peli1"         
##  [3013] "Gm24917"        "Zrsr2-ps1"      "Fer1l5"         "Cct4"          
##  [3017] "Fam161a"        "Xpo1"           "1700030C12Rik"  "Pus10"         
##  [3021] "Bcl11a"         "4933427E13Rik"  "Fancl"          "Efemp1"        
##  [3025] "Pnpt1"          "Cnnm4"          "Ccdc88a"        "Clhc1"         
##  [3029] "Gm8098"         "Asb3"           "Cpeb4"          "4930524B15Rik" 
##  [3033] "Gm12109"        "Snrnp25"        "Mpg"            "Stk10"         
##  [3037] "Cnnm3"          "Fbxw11"         "Ssbp1"          "D130052B06Rik" 
##  [3041] "Insyn2b"        "Slit3"          "Gm12129"        "Nudcd2"        
##  [3045] "Btf3-ps7"       "Atp10b"         "Slu7"           "Zap70"         
##  [3049] "Pwwp2a"         "Rnf145"         "Clint1"         "Adam19"        
##  [3053] "Garin3"         "Med7"           "Gm12176"        "Gm12181"       
##  [3057] "Rack1"          "Snord95"        "Vwa3b"          "Trim7"         
##  [3061] "Or2t26"         "Or2o1"          "Zfp62"          "Or2y1g"        
##  [3065] "Or2y1f"         "Or2y1b"         "Or2y13"         "Flt4"          
##  [3069] "Tbc1d9b"        "Cnga3"          "Mrnip"          "Mgat4b"        
##  [3073] "Cby3"           "Hnrnph1"        "Adamts2"        "Grm6"          
##  [3077] "Gm12201"        "Col23a1"        "Nhp2"           "D930048N14Rik" 
##  [3081] "Inpp4a"         "Sar1b"          "Gm26061"        "Skp1"          
##  [3085] "9530068E07Rik"  "Fstl4"          "Gdf9"           "Shroom1"       
##  [3089] "Gm9945"         "Septin8"        "Kif3a"          "Cpsf7"         
##  [3093] "Unc50"          "Irf1"           "P4ha2"          "Gm12221"       
##  [3097] "Gm12222"        "Acsl6"          "Meikin"         "Fnip1"         
##  [3101] "Hint1"          "Gpx3"           "Zic5"           "Lipt1"         
##  [3105] "Mfap3"          "Galnt10"        "Cnot8"          "Mrpl22"        
##  [3109] "Zfp692"         "Sh3bp5l"        "Trim58"         "Or2ak7"        
##  [3113] "Or2ak4"         "Or2t45"         "Pdcl3"          "Or2t44"        
##  [3117] "Or9e1"          "2810021J22Rik"  "Btnl10"         "H2bc27"        
##  [3121] "H3f4"           "Trim11"         "Gm10435"        "2310033P09Rik" 
##  [3125] "Wnt9a"          "Npas2"          "4933439C10Rik"  "Gm16062"       
##  [3129] "Nt5m"           "Med9"           "Rai1"           "Drc3"          
##  [3133] "Drg2"           "Llgl1"          "Mief2"          "Smcr8"         
##  [3137] "Cnot11"         "Dhrs7b"         "Kcnj12"         "Tnfrsf13b"     
##  [3141] "Aldh3a1"        "Mfap4"          "B9d1"           "Fam83g"        
##  [3145] "Specc1"         "Adora2b"        "Ttc19"          "Map4k4"        
##  [3149] "Pigl"           "Trpv2"          "Snord49a"       "Mmgt2"         
##  [3153] "Tvp23b"         "Cdrt4"          "Tekt3"          "Pmp22"         
##  [3157] "Elac2"          "Gm53042"        "Il1r1"          "Zkscan6"       
##  [3161] "Pirt"           "Tmem220"        "Gas7"           "Gsg1l2"        
##  [3165] "Dhrs7c"         "Stx8"           "Pik3r6"         "Mfsd6l"        
##  [3169] "Ccdc42"         "Slc9a2"         "Myh10"          "Rnf222"        
##  [3173] "Rpl26"          "Slc25a35"       "Aurkb"          "Borcs6"        
##  [3177] "Tmem107"        "Vamp2"          "Per1"           "Hes7"          
##  [3181] "Tmem182"        "Aloxe3"         "Trappc1"        "Kcnab3"        
##  [3185] "Rnf227"         "Chd3"           "Trp53"          "Sat2"          
##  [3189] "Fxr2"           "Sox15"          "Zbtb4"          "Mrps9"         
##  [3193] "G630025P09Rik"  "Plscr3"         "Gps2"           "Cldn7"         
##  [3197] "Ctdnep1"        "Gabarap"        "Phf23"          "Dvl2"          
##  [3201] "Asgr2"          "Slc16a11"       "Psph"           "AI597479"      
##  [3205] "Mir497"         "Mir195a"        "Med11"          "Zmynd15"       
##  [3209] "Tm4sf5"         "Psmb6"          "Mink1"          "Rnf167"        
##  [3213] "Eno3"           "Kif1c"          "Nck2"           "Zfp3"          
##  [3217] "Rabep1"         "Rpain"          "Mis12"          "Wscd1"         
##  [3221] "Pimreg"         "Txndc17"        "4930563E22Rik"  "Ggt6"          
##  [3225] "Mybbp1a"        "Ecrg4"          "Ankfy1"         "Ncbp3"         
##  [3229] "Itgae"          "P2rx5"          "Shpk"           "Trpv1"         
##  [3233] "Spata22"        "Or1e17"         "Or3a1b"         "Or3a1c"        
##  [3237] "Gm19587"        "Ccdc92b"        "Cluh"           "Mettl16"       
##  [3241] "Tsr1"           "Smg6"           "Mir212"         "Mir132"        
##  [3245] "Rtn4rl1"        "Rilp"           "Scarf1"         "Ercc5"         
##  [3249] "Myo1c"          "Crk"            "Tlcd3a"         "Dbil5"         
##  [3253] "Mrm3"           "Bhlha9"         "Trarg1"         "Tmigd1"        
##  [3257] "Slc6a4"         "Ssh2"           "Col3a1"         "Git1"          
##  [3261] "Gm11191"        "Myo18a"         "Sez6"           "Phf12"         
##  [3265] "Dhrs13"         "Flot2"          "Fam222b"        "Proca1"        
##  [3269] "Sdf2"           "Wdr75"          "Rskr"           "Spag5"         
##  [3273] "Aldoc"          "Pigs"           "Unc119"         "Slc46a1"       
##  [3277] "Vtn"            "Sebox"          "Ift20"          "Lyrm9"         
##  [3281] "Dnah7b"         "Gm11201"        "Rab11fip4"      "Mir193a"       
##  [3285] "Mir365-2"       "Atad5"          "Rhot1"          "Rhbdl3"        
##  [3289] "Zfp207"         "Cdk5r1"         "Tmem98"         "n-R5s211"      
##  [3293] "Spaca3"         "Tmem132e"       "Gm11426"        "Zfp830"        
##  [3297] "1700020L24Rik"  "Taf15"          "E230016K23Rik"  "Ccl4"          
##  [3301] "Wfdc17"         "Wfdc21"         "Gm8357"         "Ddx52"         
##  [3305] "Synrg"          "Ggnbp2os"       "Myo19"          "Chct1"         
##  [3309] "Tbx2"           "Tbx4"           "Brip1os"        "Rnft1"         
##  [3313] "Tubd1"          "Ube2r2"         "Gm8384"         "Ptrh2"         
##  [3317] "Ska2"           "Trim37"         "Rnf43"          "Mks1"          
##  [3321] "Srsf1"          "Vezf1"          "Mrps23"         "2210409E12Rik" 
##  [3325] "Coil"           "Stat1"          "Trim25"         "Dgkeos"        
##  [3329] "Cox11"          "Gm11502"        "Tob1"           "Ankrd40"       
##  [3333] "Spata20"        "Lrrc59"         "Mrpl27"         "Cdc34b"        
##  [3337] "Nemp2"          "Col1a1"         "Ppp1r9b"        "Slc35b1"       
##  [3341] "B130006D01Rik"  "Phospho1"       "Gngt2"          "Gip"           
##  [3345] "Snf8"           "Hoxb9"          "Hoxb8"          "Hibch"         
##  [3349] "Hoxb7"          "Hoxb3"          "Hoxb1"          "Copz2"         
##  [3353] "Prr15l"         "Scrn2"          "Osbpl7"         "Mrpl45"        
##  [3357] "Socs7"          "Arhgap23"       "Ormdl1"         "Psmb3"         
##  [3361] "Lasp1"          "B230217C12Rik"  "Cdk12"          "Ppp1r1b"       
##  [3365] "Erbb2"          "Grb7"           "Lrrc3c"         "Gsdma3"        
##  [3369] "Gsdma"          "Osgepl1"        "Csf3"           "Msl1"          
##  [3373] "Casc3"          "Wipf2"          "Cdc6"           "Rara"          
##  [3377] "Igfbp4"         "Krtap31-3"      "Gm11560"        "Eif1"          
##  [3381] "Ccdc150"        "Gast"           "Fkbp10"         "Odad4"         
##  [3385] "Cnp"            "Hspb9"          "Atp6v0a1"       "Naglu"         
##  [3389] "Coasy"          "Mlx"            "Tubg1"          "Mob4"          
##  [3393] "Tubg2"          "Ramp2"          "Vps25"          "Cntd1"         
##  [3397] "Aoc2"           "Rnd2"           "Tmem106a"       "Rdm1"          
##  [3401] "Arl4d"          "4930417O22Rik"  "Mars2"          "Cfap97d1"      
##  [3405] "Cd300lg"        "Ppih"           "Nags"           "Hrob"          
##  [3409] "Tmub2"          "Rundc3a"        "Grn"            "Mdk-ps1"       
##  [3413] "Adam11"         "Rps24"          "Hexim2"         "Fmnl1"         
##  [3417] "Wnt3"           "Arf2"           "Myl4"           "Itgb3"         
##  [3421] "Efcab3"         "Tlk2"           "Mrc2"           "Tanc2"         
##  [3425] "Smim7"          "1700066M21Rik"  "Gm9910"         "Ace"           
##  [3429] "Kcnh6"          "Map3k3"         "Prr29"          "Snord104"      
##  [3433] "Cep95"          "Psmd12"         "Apoh"           "Gm11667"       
##  [3437] "Maip1"          "Cep112"         "Axin2"          "9930022D16Rik" 
##  [3441] "Prkar1a"        "Gm11675"        "Sox9"           "4933434M16Rik" 
##  [3445] "Cog1"           "Mtnap1"         "Gm11691"        "Sgo2a"         
##  [3449] "Ttyh2"          "Dnai2"          "Kif19a"         "Gprc5c"        
##  [3453] "Cd300a"         "Nherf1"         "Tmem104"        "Cdr2l"         
##  [3457] "Mrpl58"         "Kctd2"          "Aox3"           "Trim80"        
##  [3461] "Armc7"          "Nup85"          "Mrps7"          "Gm23699"       
##  [3465] "Tsen54"         "Llgl2"          "Myo15b"         "Erln"          
##  [3469] "Sap30bp"        "Aox4"           "Itgb4"          "Unk"           
##  [3473] "Ten1"           "Rps11-ps2"      "Sphk1"          "Prcd"          
##  [3477] "BC018473"       "Mettl23"        "Septin9"        "6030468B19Rik" 
##  [3481] "Ndufb3"         "Afmid"          "Birc5"          "Tmem235"       
##  [3485] "Socs3"          "Pgs1"           "Engase"         "Enpp7"         
##  [3489] "Cbx2"           "Ccdc40"         "Gaa"            "Cflar"         
##  [3493] "Slc26a11"       "Rnf213"         "Endov"          "Chmp6"         
##  [3497] "Baiap2"         "0610009L18Rik"  "Fscn2"          "Ccdc137"       
##  [3501] "Hgs"            "Mrpl12"         "Casp8"          "Slc25a10"      
##  [3505] "Gcgr"           "Anapc11"        "Npb"            "Lrrc45"        
##  [3509] "Uts2r"          "Hexd"           "Narf"           "Foxk2"         
##  [3513] "Fn3krp"         "G730003C15Rik"  "Tbcd"           "Ptchd3"        
##  [3517] "Sfi1"           "Limk2"          "Rnf185"         "Smtn"          
##  [3521] "Tug1"           "Osbp2"          "Tcn2"           "Sec14l2"       
##  [3525] "Fzd7"           "Gm11956"        "Uqcr10"         "Nf2"           
##  [3529] "Nefh"           "Gas2l1"         "Ewsr1"          "Emid1"         
##  [3533] "Kremen1"        "Znrf3"          "Ccdc117"        "Polr2f"        
##  [3537] "Gm973"          "Mrps24"         "Urgcp"          "Pgam2"         
##  [3541] "Pold2"          "Gck"            "Camk2b"         "Nudcd3"        
##  [3545] "Rps15a-ps4"     "Npc1l1"         "Ddx56"          "Fam117b"       
##  [3549] "H2az2"          "Purb"           "Nacad"          "Gm11979"       
##  [3553] "Hus1"           "Sun3"           "Polr2c"         "Gm26458"       
##  [3557] "4930512M02Rik"  "Fignl1"         "Carf"           "Gm25058"       
##  [3561] "Cobl"           "Sec61g"         "Ublcp1"         "Gm12664"       
##  [3565] "Pno1"           "Gm12015"        "Etaa1"          "Gm12020"       
##  [3569] "Meis1"          "Nbeal1"         "Actr2"          "Aftph"         
##  [3573] "Lgalsl"         "Ugp2"           "4932414J04Rik"  "Mdh1"          
##  [3577] "Otx1"           "Gm12058"        "Commd1"         "1700093K21Rik" 
##  [3581] "Cyp20a1"        "Selenok-ps1"    "Pex13"          "Papolg"        
##  [3585] "A830031A19Rik"  "5730522E02Rik"  "6820445E23Rik"  "Vrk2"          
##  [3589] "Cyb5d1"         "Cfap36"         "Fem1al"         "Abi2"          
##  [3593] "Cimip6"         "Acyp2"          "Stc2"           "Bod1"          
##  [3597] "Il9r"           "Rhbdf1"         "Nprl3"          "Efcab9"        
##  [3601] "Smim23"         "Fgf18"          "Eif4a1"         "Npm1"          
##  [3605] "Tlx3"           "Ranbp17"        "Anp32-ps"       "Foxi1"         
##  [3609] "Dock2"          "Rars1"          "Wwc1"           "Tenm2"         
##  [3613] "Gm6644"         "Pard3b"         "Mat2b"          "Hmmr"          
##  [3617] "Ccng1"          "Gabra1"         "Pttg1"          "Gm12151"       
##  [3621] "Ttc1"           "Adra1b"         "Thg1l"          "Sft2d1"        
##  [3625] "Gm11599"        "Gm12186"        "Btnl9"          "Cnot6"         
##  [3629] "Sqstm1"         "Rufy1"          "Zfp354c"        "Zfp354b"       
##  [3633] "4933414I15Rik"  "Msantd5l"       "Rmnd5b"         "Eef1b2"        
##  [3637] "N4bp3"          "Sec24a"         "Jade2"          "Or2y7"         
##  [3641] "Tcf7"           "Hspa4"          "Leap2"          "Uqcrq"         
##  [3645] "Gm9837"         "Il13"           "Eif5"           "Mir686"        
##  [3649] "Adam23"         "Rad50"          "Gm17334"        "Slc22a5"       
##  [3653] "Slc22a4"        "Pdlim4"         "Lyrm7"          "Tnip1"         
##  [3657] "Anxa6"          "Atp5pb"         "Slc36a3"        "Crygf"         
##  [3661] "Fat2"           "Sparc"          "Fam114a2"       "Hand1"         
##  [3665] "Or2z2"          "Cfap144"        "Zfp39"          "H2bc26"        
##  [3669] "Obscn"          "Iba57"          "Unc80"          "Guk1"          
##  [3673] "Arf1"           "Wnt3a"          "Zfp867"         "Zkscan17"      
##  [3677] "Or2b11"         "Gm12261"        "Pld6"           "Rasd1"         
##  [3681] "Pemt"           "Rpe"            "4930412M03Rik"  "Srebf1"        
##  [3685] "Tom1l2"         "Atpaf2"         "Gm12620"        "Flii"          
##  [3689] "Top3a"          "Shmt1"          "Tmem11"         "Map2k3os"      
##  [3693] "Gm23422"        "Usp22"          "Slc47a2"        "Slc47a1"       
##  [3697] "Rnf112"         "Mapk7"          "B9d1os"         "Prpsap2"       
##  [3701] "A530017D24Rik"  "Akap10"         "Zswim7"         "Vwc2l"         
##  [3705] "Zfp287"         "Wsb2-ps"        "Zfp286"         "Hs3st3b1"      
##  [3709] "Cox10"          "Arhgap44"       "Map2k4"         "Gm12298"       
##  [3713] "Adprm"          "Glp2r"          "Atic"           "Usp43"         
##  [3717] "Ntn1"           "Ndel1"          "Odf4"           "9130213A22Rik" 
##  [3721] "Cntrob"         "Tmem88"         "Efnb3"          "Wrap53"        
##  [3725] "Atp1b2"         "Xrcc5"          "Shbg"           "Mpdu1"         
##  [3729] "Cd68"           "Senp3"          "Slc35g3"        "Nlgn2"         
##  [3733] "Tnk1"           "Kctd11"         "Acap1"          "2810408A11Rik" 
##  [3737] "Igfbp2"         "Slc2a4"         "Acadvl"         "Bcl6b"         
##  [3741] "Rnasek"         "Alox12"         "Alox15"         "Pelp1"         
##  [3745] "Cxcl16"         "Chrne"          "Slc25a11"       "Gpbar1"        
##  [3749] "Pfn1"           "Spag7"          "Inca1"          "C1qbp"         
##  [3753] "Dhx33"          "Derl2"          "Gm12321"        "Nlrp1c-ps"     
##  [3757] "Med31"          "Tekt1"          "Hdac5"          "Pnkd"          
##  [3761] "Spns2"          "Spns3"          "Gm24143"        "Haspin"        
##  [3765] "Emc6"           "Ctns"           "Or1e21"         "Or3a1d"        
##  [3769] "Rpa1"           "Serpinf1"       "Catip"          "Serpinf2"      
##  [3773] "Doc2b"          "Rph3al"         "Vps53"          "Gemin4"        
##  [3777] "Glod4"          "Abr"            "Gosr1"          "Cpd"           
##  [3781] "Nsrp1"          "Slc11a1"        "Mir423"         "Trp53i13"      
##  [3785] "Gm10392"        "Taok1"          "Gm11190"        "Dhrs13os"      
##  [3789] "Eral1"          "Lsm6"           "Traf4"          "Nek8"          
##  [3793] "Ctdsp1"         "Snord42b"       "Supt6"          "Foxn1"         
##  [3797] "Tmem199"        "Tnfaip1"        "Tmem97"         "Nlk"           
##  [3801] "Gm11197"        "Ccnq"           "Lgals9"         "Mir26b"        
##  [3805] "Ksr1"           "Wsb1"           "Omg"            "Utp6"          
##  [3809] "Crlf3"          "5730455P16Rik"  "Myo1d"          "Asic2"         
##  [3813] "Cct6b"          "Rad51d"         "Bcs1l"          "Unc45bos"      
##  [3817] "Slfn5os"        "Pex12"          "Mmp28"          "Heatr9"        
##  [3821] "Ccl5"           "Rpl9"           "Dusp14"         "Aatf"          
##  [3825] "Lhx1"           "Cyp27a1"        "Mrm1"           "Dhrs11"        
##  [3829] "Pigw"           "Appbp2"         "Gm57365"        "Gm11444"       
##  [3833] "Ints2"          "Rps6kb1"        "Gm9975"         "Rpl13a"        
##  [3837] "Wnt6"           "Dhx40"          "Smg8"           "Prr11"         
##  [3841] "Gm22883"        "Epx"            "Or4d2b"         "Or4d2"         
##  [3845] "Dynll2"         "Akap1"          "Scpep1"         "Wnt10a"        
##  [3849] "Elobl"          "Dgke"           "Ankfn1"         "Pctp"          
##  [3853] "Hlf"            "Stxbp4"         "Tom1l1"         "Utp18"         
##  [3857] "Nme2"           "Nme1"           "Cdk5r2"         "Rpl27"         
##  [3861] "Wfikkn2"        "Luc7l3"         "Mycbpap"        "Rsad1"         
##  [3865] "Eme1"           "Xylt2"          "Gm11545"        "Sgca"          
##  [3869] "Pdk2"           "Atp6v0d1"       "Ankzf1"         "Itga3"         
##  [3873] "Nxph3"          "Ngfr"           "Zfp652os"       "Gm11536"       
##  [3877] "Gm11529"        "Snx11"          "Nfe2l1"         "Cdk5rap3"      
##  [3881] "Sp2"            "Stk16"          "Tbkbp1"         "4933428G20Rik" 
##  [3885] "Epop"           "Pcgf2"          "Pip4k2b"        "Spmap1"        
##  [3889] "Fbxo47"         "Plxdc1"         "Cacnb1"         "Stac2"         
##  [3893] "Speg"           "Fbxl20"         "Neurod2"        "Mien1"         
##  [3897] "Ormdl3"         "Nr1d1"          "Gm12359"        "Gjd3"          
##  [3901] "Ccr7"           "Smarce1"        "Krt222"         "Gmppa"         
##  [3905] "Krt12"          "Krtap3-2"       "Krtap3-1"       "Krtap1-5"      
##  [3909] "Krtap1-4"       "Krtap1-3"       "Krtap9-3"       "Krtap4-2"      
##  [3913] "Krtap4-7"       "Krtap4-24"      "Asic4"          "Krtap4-25"     
##  [3917] "Krtap4-26"      "Krtap17-1"      "Krt33b"         "Krt34"         
##  [3921] "Krt31"          "Krt42"          "Hap1"           "Atp5mc1"       
##  [3925] "Jup"            "Stk11ip"        "P3h4"           "Klhl11"        
##  [3929] "Dnajc7"         "Zfp385c"        "Dhx58"          "Kat2a"         
##  [3933] "Rab5c"          "Hcrt"           "Stat5b"         "Stat3"         
##  [3937] "Slc4a3"         "Psmc3ip"        "Ccr10"          "Coa3"          
##  [3941] "Aarsd1"         "Ptges3l"        "Vat1"           "Brca1"         
##  [3945] "Meox1"          "Sost"           "Mpp3"           "Gm5257"        
##  [3949] "Ppy"            "Pyy"            "Tmem101"        "Atxn7l3"       
##  [3953] "Ubtf"           "Fam171a2"       "Gpatch8"        "Ccdc43"        
##  [3957] "Eftud2"         "Gfap"           "Sgpp2"          "Kif18b"        
##  [3961] "C1ql1"          "Dcakd"          "Plcd3"          "Spata32"       
##  [3965] "Arhgap27"       "Plekhm1"        "Lrrc37a"        "Lrrc37"        
##  [3969] "Lyzl6"          "Acsl3"          "Gosr2"          "Wnt9b"         
##  [3973] "Nsf"            "Kansl1"         "Cyb561"         "Ccdc47"        
##  [3977] "Ftsj3"          "Smarcd2"        "Cd79b"          "Ern1"          
##  [3981] "Gm49705"        "Kcne4"          "Polg2"          "Smurf2"        
##  [3985] "Gm11708"        "Nol11"          "Cacng1"         "Cacng4"        
##  [3989] "Cacng5"         "Prkca"          "Slc16a6"        "Fam20a"        
##  [3993] "Nyap2"          "Abca5"          "Gm11681"        "Vcf1"          
##  [3997] "Cpsf4l"         "Sdk2"           "4932435O22Rik"  "Btbd17"        
##  [4001] "Cd300e"         "Cd300lf"        "Nat9"           "Rhbdd1"        
##  [4005] "Fdxr"           "Fads6"          "Ush1g"          "Hid1"          
##  [4009] "Nt5c"           "Jpt1"           "Sumo2"          "Gga3"          
##  [4013] "Mif4gd"         "Slc25a19"       "Gm54925"        "Grb2"          
##  [4017] "Galk1"          "Wbp2"           "Trim65"         "Mrpl38"        
##  [4021] "Fbf1"           "Acox1"          "Srp68"          "Exoc7"         
##  [4025] "Foxj1"          "Daw1"           "Qrich2"         "Ube2o"         
##  [4029] "Cygb"           "Mxra7"          "Jmjd6"          "Srsf2"         
##  [4033] "Tmc6"           "Tk1"            "Usp36"          "Dnah17"        
##  [4037] "Fbxo36"         "Cyth1"          "Timp2"          "Lgals3bp"      
##  [4041] "Cant1"          "Rbfox3"         "Cbx8"           "Cbx4"          
##  [4045] "Tbc1d16"        "Eif4a3"         "Nptx1"          "Itm2c"         
##  [4049] "Aatk"           "Mir338"         "Cep131"         "Slc38a10"      
##  [4053] "Reno1"          "Faap100"        "Oxld1"          "Mcrip1"        
##  [4057] "Ppp1r27"        "P4hb"           "4933407L21Rik"  "Arhgdia"       
##  [4061] "Alyref"         "Pcyt2"          "Sirt7"          "Mafg"          
##  [4065] "Pycr1"          "Cenpx"          "Dcxr"           "Cbr2"          
##  [4069] "Rfng"           "2810459M11Rik"  "Dus1l"          "Fasn"          
##  [4073] "Ccdc57"         "Tex19.2"        "Ogfod3"         "Cybc1"         
##  [4077] "Wdr45b"         "Rab40b"         "B3gntl1"        "Rab10os"       
##  [4081] "B3gnt7"         "Kif3c"          "Dtnb"           "Dnmt3a"        
##  [4085] "Ptrhd1"         "Sf3b6"          "Atad2b"         "2810032G03Rik" 
##  [4089] "Nfyc"           "Apob"           "Ldah"           "Dlg1"          
##  [4093] "C130036L24Rik"  "Sdc1"           "Acaca"          "Rdh14"         
##  [4097] "Smc6"           "Cyria"          "Gm9202"         "Ntsr2"         
##  [4101] "E2f6"           "Rock2"          "Nol10"          "Cops7b"        
##  [4105] "Odc1"           "Gm22748"        "Hpcal1"         "1700030C10Rik" 
##  [4109] "Bnip3l"         "5730507C01Rik"  "2410018L13Rik"  "Gm4983"        
##  [4113] "Gm5784"         "9030624G23Rik"  "Prss56"         "Asap2"         
##  [4117] "Cpsf3"          "Iah1"           "Gm49251"        "Taf1b"         
##  [4121] "Klf11"          "Rrm2"           "Kidins220"      "Cmpk2"         
##  [4125] "Rnaseh1"        "Chrng"          "Adi1"           "Eipr1"         
##  [4129] "Pxdn"           "Tmem18"         "Sh3yl1"         "Lamb1"         
##  [4133] "Gm9359"         "Gm25913"        "Ccdc71l"        "Gm18726"       
##  [4137] "Eif4e2"         "Nampt"          "Gdap10"         "Sypl1"         
##  [4141] "Atxn7l1"        "Efcab10"        "Polr1f"         "Prps1l1"       
##  [4145] "Ube2frt"        "Ankmy2"         "Sostdc1"        "Efhd1"         
##  [4149] "Etv1"           "Gm7008"         "Gm7242"         "Pnpla8"        
##  [4153] "Rps11-ps4"      "G2e3"           "Ap4s1"          "Gm5785"        
##  [4157] "Nubpl"          "Arhgap5"        "Snorc"          "Akap6"         
##  [4161] "Gm47553"        "Prorp"          "Psma6"          "Aldoart2"      
##  [4165] "Insm2"          "Pax9"           "Mipol1"         "Ttc6"          
##  [4169] "Gemin2"         "Inpp5d"         "Pnn"            "Mia2"          
##  [4173] "Gm7719"         "Gm30738"        "Gm527"          "Togaram1"      
##  [4177] "Prpf39"         "Wdr20rt"        "Lrr1"           "Mgat2"         
##  [4181] "Atg16l1"        "9330151L19Rik"  "Klhdc1"         "Arf6"          
##  [4185] "4930512B01Rik"  "Gm3086"         "Tmx1"           "Frmd6"         
##  [4189] "Gm10457"        "Psma3"          "Arid4a"         "Dgkd"          
##  [4193] "Tomm20l"        "2700049A03Rik"  "Dact1"          "Daam1"         
##  [4197] "Jkamp"          "Mnat1"          "Slc38a6"        "Hif1a"         
##  [4201] "S100a11-ps"     "Snapc1"         "Tmem216"        "Mroh2a"        
##  [4205] "Rhoj"           "Syne2"          "Mthfd1"         "Akap5"         
##  [4209] "Ppp1r36"        "Ppp1r36dn"      "Churc1"         "Gm25926"       
##  [4213] "Ccdc196"        "Gphn"           "Trpm8"          "Eif2s1"        
##  [4217] "Rad51b"         "Exd2"           "Slc39a9"        "Plekhd1"       
##  [4221] "Susd6"          "Srsf5"          "Smoc1"          "Ttc9"          
##  [4225] "Rbm25"          "Sh3bp4"         "Papln"          "Riox1"         
##  [4229] "Acot2"          "Dnal1"          "Coq6"           "Bbof1"         
##  [4233] "Rnf113a2"       "Lin52"          "Isca2"          "Fcf1"          
##  [4237] "Agap1"          "Ylpm1"          "Dlst"           "Eif2b2"        
##  [4241] "Zc2hc1c"        "Jdp2"           "Batf"           "Flvcr2"        
##  [4245] "Vash1"          "Lrrc74a"        "Tmem63c"        "Mlph"          
##  [4249] "Gstz1"          "Ahsa1"          "Slirp"          "Eif1ad18"      
##  [4253] "Nrxn3"          "Tshr"           "Gm6869"         "Ttc8"          
##  [4257] "Kcnk13"         "Gm10433"        "Prlh"           "Gm10432"       
##  [4261] "A630072L19Rik"  "D130020L05Rik"  "Kif4-ps"        "Chga"          
##  [4265] "Ubr7"           "Cox8c"          "Fam181a"        "Ifi27"         
##  [4269] "Serpina5"       "Scly"           "Serpina3a"      "Serpina3f"     
##  [4273] "Serpina3n"      "4930408O17Rik"  "Glrx5"          "Bdkrb2"        
##  [4277] "Bdkrb1"         "Gskip"          "Cyp46a1"        "Evl"           
##  [4281] "Espnl"          "Mir342"         "Yy1"            "Mir345"        
##  [4285] "Slc25a47"       "Wdr25"          "Mif-ps7"        "Dlk1"          
##  [4289] "Meg3"           "Mir673"         "Mir337"         "Erfe"          
##  [4293] "Mir665"         "6430411K18Rik"  "Mir341"         "Mir370"        
##  [4297] "Mir494"         "Mir679"         "Mir666"         "Mir667"        
##  [4301] "Mir668"         "Gm9661"         "Traf3ip1"       "Ppp2r5c"       
##  [4305] "Wdr20"          "Tecpr2"         "Rcor1"          "Amn"           
##  [4309] "Exoc3l4"        "Tnfaip2"        "Snora28"        "Coa8"          
##  [4313] "Aspg"           "Ythdf1"         "Asb1"           "Kif26a"        
##  [4317] "A530016L24Rik"  "Inf2"           "Adss1"          "Siva1"         
##  [4321] "Zbtb42"         "Cep170b"        "Clba1"          "9230104M06Rik" 
##  [4325] "Pacs2"          "Or9s23"         "Tex22"          "Mta1"          
##  [4329] "Crip2"          "Crip1"          "Tedc1"          "Adam6a"        
##  [4333] "Zfp386"         "Vipr2"          "Esyt2"          "Ncapg2"        
##  [4337] "Or9s15"         "Rapgef5"        "Cdca7l"         "Ncoa4"         
##  [4341] "Tmem196"        "Rab10"          "1110002L01Rik"  "Rps7-ps2"      
##  [4345] "Dnmt3aos"       "Ncoa1"          "Fam228a"        "Or9s14"        
##  [4349] "Fam228b"        "Mfsd2b"         "Ubxn2a"         "Klhl29"        
##  [4353] "Gm46311"        "Gdf7"           "Rhob"           "Pgk1"          
##  [4357] "Kcns3"          "Msgn1"          "Or9s13"         "Gen1"          
##  [4361] "Gm4803"         "Rpl21-ps2"      "Ddx1"           "Gm4929"        
##  [4365] "Lratd1"         "Trib2"          "Lpin1"          "Greb1"         
##  [4369] "Cimip5"         "Gpr35"          "Zfp125"         "3110053B16Rik" 
##  [4373] "Itgb1bp1"       "Adam17"         "Ywhaq"          "Gm19924"       
##  [4377] "Gm49929"        "Gm20472"        "Gm16372"        "Id2"           
##  [4381] "Gpc1"           "Silc1"          "Sox11"          "Dcdc2c"        
##  [4385] "Allc"           "Colec11"        "Rps7"           "Trappc12"      
##  [4389] "Acp1"           "Dld"            "Cbll1"          "Mir149"        
##  [4393] "Dus4l"          "Hbp1"           "Prkar2b"        "Pik3cg"        
##  [4397] "Gm54696"        "Hdac9"          "Mir680-3"       "Ahr"           
##  [4401] "Tspan13"        "Bzw2"           "Dusp28"         "Lrrc72"        
##  [4405] "Crppa"          "Gm4257"         "Ifrd1"          "Zfp277"        
##  [4409] "Nova1"          "Gm7172"         "Strn3"          "Heatr5a"       
##  [4413] "Dtd2"           "Rnpepl1"        "Sptssa"         "Eapp"          
##  [4417] "Snx6"           "2700097O09Rik"  "Gm7511"         "Ppp2r3c"       
##  [4421] "Ralgapa1"       "Mbip"           "Nkx2-1"         "Slc25a21"      
##  [4425] "Ube2v1"         "Aqp12"          "Foxa1"          "Sec23a"        
##  [4429] "Trappc6b"       "Rpl7a-ps1"      "Klhl28"         "Fkbp3"         
##  [4433] "Mis18bp1"       "Rpl10l"         "Mdga2"          "Dnaaf2"        
##  [4437] "Sned1"          "Nemf"           "Gm9887"         "Vcpkmt"        
##  [4441] "Sos2"           "L2hgdh"         "Cdkl1"          "Mir681"        
##  [4445] "Map4k5"         "Gm23579"        "Nin"            "Ppp1r7"        
##  [4449] "Pygl"           "Gpr135"         "Ccdc175"        "Rtn1"          
##  [4453] "Dhrs7"          "4930447C04Rik"  "Six1"           "Six4"          
##  [4457] "D830013O20Rik"  "Tmem30b"        "Ano7"           "Ppp2r5e"       
##  [4461] "Wdr89"          "Gm7862"         "Tex21"          "Zbtb25"        
##  [4465] "Sptb"           "Gm4864"         "Atp6v1d"        "Pigh"          
##  [4469] "Vti1b"          "Farp2"          "Zfyve26"        "Gm8275"        
##  [4473] "Zfp36l1"        "Actn1"          "Dcaf5"          "Adam4"         
##  [4477] "Adam21"         "Med6"           "Dpf3"           "Zfyve1"        
##  [4481] "Bok"            "Heatr4"         "Gm26571"        "Gm8385"        
##  [4485] "Pnma1"          "Gm5436"         "Entpd5"         "Aldh6a1"       
##  [4489] "Syndig1l"       "Prox2"          "Rps6kl1"        "Gm10550"       
##  [4493] "Mlh3"           "Acyp1"          "Erg28"          "Tgfb3"         
##  [4497] "Irf2bpl"        "Zdhhc22"        "Tmed8"          "Noxred1"       
##  [4501] "Vipas39"        "Ism2"           "Atg4b"          "Sptlc2"        
##  [4505] "Alkbh1"         "Cep128"         "Gtf2a1"         "Sel1l"         
##  [4509] "Lysmd1"         "Gm4808"         "1700019M22Rik"  "Kcnk10"        
##  [4513] "Ptpn21"         "Ing5"           "Eml5"           "Foxn3"         
##  [4517] "Efcab11"        "Nrde2"          "Ttc7b"          "Gpr68"         
##  [4521] "Ccdc88c"        "Ppp4r3a"        "Tc2n"           "Fbln5"         
##  [4525] "D2hgdh"         "Ndufb1"         "Lgmn"           "Itpk1"         
##  [4529] "Prima1"         "Asb2"           "Ifi27l2b"       "Serpina3c"     
##  [4533] "Gsc"            "Dicer1"         "Syne3"          "Gbf1"          
##  [4537] "Fam174a"        "Atg2b"          "Bcl11b"         "Setd3"         
##  [4541] "Degs2"          "Mok"            "Ankrd9"         "Cdc42bpb"      
##  [4545] "Gm10425"        "Gm266"          "Ckb"            "Gin1"          
##  [4549] "Bag5"           "Ppp1r13b"       "Atp5mj"         "Tmem179"       
##  [4553] "Akt1"           "Ahnak2"         "Cdca4"          "Gpr132"        
##  [4557] "Brf1"           "Ighv5-7"        "Slco6d1"        "Igh-VX24"      
##  [4561] "V165-D-J-C mu"  "Ighv1-72"       "Gm9238"         "Ighv1-83"      
##  [4565] "Ighv1-84"       "Gm9260"         "Dync2i1"        "Dnah11"        
##  [4569] "Sp4"            "Cntnap5b"       "Gm54747"        "Gm8598"        
##  [4573] "Speer6-ps1"     "Gdi2"           "Calm4"          "Klf6"          
##  [4577] "Pitrm1"         "Gm5191"         "Idi1"           "Dip2c"         
##  [4581] "Relch"          "Heatr1"         "Nid1"           "Lyst"          
##  [4585] "Gng4"           "B3galnt2"       "Arid4b"         "Psma2"         
##  [4589] "AW209491"       "Gm25020"        "Mplkip"         "Tnfrsf11a"     
##  [4593] "Gpank1"         "Yae1d1"         "Vps41"          "Amph"          
##  [4597] "Elmo1"          "Gm7614"         "Gm54437"        "Gpx6"          
##  [4601] "Zscan12"        "Isca1"          "Zcchc2"         "H2bc14"        
##  [4605] "H2bc22"         "Zfp184"         "H4c8"           "H3c4"          
##  [4609] "H4c4"           "H2bc4"          "H1f2"           "H2bc3"         
##  [4613] "H1f1"           "Gm6651"         "Trim38"         "H2ac1"         
##  [4617] "BC005537"       "Tdp2"           "D130043K22Rik"  "Dcdc2a"        
##  [4621] "Prl2c1"         "Gm11360"        "Agtr1a"         "Dusp22"        
##  [4625] "Nifk"           "Gm5447"         "Foxq1"          "Serpinb6b"     
##  [4629] "Ripk1"          "Fam50b"         "Prpf4b"         "Gm22126"       
##  [4633] "Ppp1r3g"        "Ly86"           "Rreb1"          "Tfcp2l1"       
##  [4637] "Riok1"          "Snrnp48"        "Pak1ip1"        "Tmem14c"       
##  [4641] "Phactr1"        "Nol7"           "Rnf182"         "Cd83"          
##  [4645] "Mylip"          "Rbm24"          "Gm42572"        "Gm8321"        
##  [4649] "Cap2"           "Rnf144b"        "Id4"            "Barx1"         
##  [4653] "Fam120aos"      "Ninj1"          "Ippk"           "Tes3-ps"       
##  [4657] "Ogn"            "Iars1"          "Tmem185b"       "Fbxw17"        
##  [4661] "S1pr3"          "Cks2"           "Gm22806"        "Secisbp2"      
##  [4665] "Gadd45g"        "Sfxn1"          "Hrh2"           "Cplx2"         
##  [4669] "Simc1"          "3110009E18Rik"  "Higd2a"         "Faf2"          
##  [4673] "Eif4e1b"        "Unc5a"          "Zfp346"         "Fgfr4"         
##  [4677] "Slc34a1"        "BC038268"       "Grk6"           "Prr7"          
##  [4681] "C1ql2"          "Tmed9"          "B4galt7"        "Caml"          
##  [4685] "Ddx46"          "Txndc15"        "Pcbd2"          "Tgfbi"         
##  [4689] "Smad5"          "Idnk"           "Rmi1"           "Ccdc93"        
##  [4693] "Naa35"          "Dapk1"          "Carnmt1"        "Gm3338"        
##  [4697] "Me1"            "Aopep"          "Ercc6l2"        "Habp4"         
##  [4701] "Cdk20"          "Gm4810"         "Slc35f5"        "Spata31"       
##  [4705] "Spata31d1c"     "Zfp369"         "Zfp1000"        "Cbx3"          
##  [4709] "Zfp997"         "Ramacl"         "Zfp759"         "Rsl1"          
##  [4713] "Zfp273"         "Gpr39"          "Krbox5"         "BC048507"      
##  [4717] "Fastkd3"        "Gm4812"         "Irx2"           "Mrpl36"        
##  [4721] "Lpcat1"         "Slc12a7"        "Brd9"           "Zdhhc11"       
##  [4725] "Gm23734"        "Ccdc127"        "Erap1"          "Hnrnpa1l2-ps"  
##  [4729] "Pcsk1"          "Gm19095"        "Spata9"         "Skic3"         
##  [4733] "2210408I21Rik"  "Arb2a"          "Gm8371"         "Ccnt2"         
##  [4737] "Lysmd3"         "Mblac2"         "Cetn3"          "Mef2c"         
##  [4741] "Ndufc1"         "Gm5452"         "Tmem161b"       "Ccnh"          
##  [4745] "Gm8526"         "Gm5667"         "Ubxn4"          "Tmem167"       
##  [4749] "Ssbp2"          "Acot12"         "Dhfr"           "Serinc5"       
##  [4753] "Mtx3"           "Homer1"         "Arsb"           "Tbca"          
##  [4757] "Otp"            "Dcdc2b"         "Derl1"          "Thsd7b"        
##  [4761] "Wdr41"          "Zbed3"          "Poc5"           "Gcnt4"         
##  [4765] "Fam169a"        "Enc1"           "Ankra2"         "Gm9828"        
##  [4769] "Gm4815"         "Zfp366"         "Yod1"           "Mrps27"        
##  [4773] "Ak6"            "4932411K12Rik"  "Cd180"          "Sgtb"          
##  [4777] "Trim23"         "Cenpk"          "Srek1ip1"       "Gm4938"        
##  [4781] "Nt5el"          "Fcmr"           "Dimt1"          "Smim15"        
##  [4785] "Gm41056"        "Rps3a3"         "Actbl2"         "Mier3"         
##  [4789] "Il6st"          "Slc38a9"        "Dhx29"          "Ccno"          
##  [4793] "Slc41a1"        "Mcidas"         "Cdc20b"         "Mir449c"       
##  [4797] "Mir449a"        "Arl15"          "4930544M13Rik"  "Mocs2"         
##  [4801] "Gm10734"        "Gm29767"        "Emb"            "Nucks1"        
##  [4805] "Gm9633"         "B430218F22Rik"  "4833420G17Rik"  "Tmem267"       
##  [4809] "Calml3"         "Net1"           "Akr1e1"         "Pfkp"          
##  [4813] "Gm10357"        "Wdr37"          "Slc45a3"        "Zmynd11"       
##  [4817] "Gm16419"        "Actn2"          "Gpr137b"        "Hnrnpf"        
##  [4821] "Tbce"           "Ggps1"          "Hecw1"          "Mrpl32"        
##  [4825] "Sugct"          "Elk4"           "Cdk13"          "Rala"          
##  [4829] "Stard3nl"       "Epdr1"          "Pgbd1"          "Zscan26"       
##  [4833] "Nkapl"          "Cox5b"          "Zfp389"         "H2ac15"        
##  [4837] "Lemd1"          "H1f5"           "H4c9"           "Vmn1r190-ps"   
##  [4841] "Zfp322a"        "Abt1"           "H2bc9"          "H4c6"          
##  [4845] "H2ac8"          "H4c3"           "4930558J22Rik"  "Gm7241"        
##  [4849] "Gm11337"        "Slc17a4"        "H2bc1"          "Scgn"          
##  [4853] "Carmil1"        "Gmnn"           "Acot13"         "Aldh5a1"       
##  [4857] "Mrs2"           "Gm11349"        "Klhdc8a"        "Sox4"          
##  [4861] "E2f3"           "Uqcrfs1"        "Hus1b"          "1700018A04Rik" 
##  [4865] "Gmds"           "D930007J09Rik"  "Serpinb9c"      "Serpinb6a"     
##  [4869] "Tubb2a"         "Gm22079"        "Nuak2"          "Pxdc1"         
##  [4873] "Fam217a"        "Eci2"           "Rpp40"          "Nrn1"          
##  [4877] "F13a1"          "Ssr1"           "Txndc5"         "Bloc1s5"       
##  [4881] "Eef1e1"         "Dstyk"          "Slc35b3"        "Rps17-ps1"     
##  [4885] "Nedd9"          "Adtrp"          "Tbc1d7"         "Dtnbp1"        
##  [4889] "Atxn1"          "Kif13a"         "Nhlrc1"         "Tpmt"          
##  [4893] "Rbbp5"          "Dek"            "Zfp169"         "Phf2"          
##  [4897] "Susd3"          "Cenpp"          "Shc3"           "Sema4d"        
##  [4901] "Auh"            "Ror2"           "Gm38564"        "Tmem81"        
##  [4905] "Drd1"           "4833439L19Rik"  "Nop16"          "Cltb"          
##  [4909] "Rnf44"          "Sncb"           "Uimc1"          "Rab24"         
##  [4913] "Mxd3"           "Lman2"          "Gm10538"        "Pfn3"          
##  [4917] "F12"            "Dbn1"           "Ddx41"          "Fam193b"       
##  [4921] "4930451E10Rik"  "Pitx1"          "Spock1"         "Klhl3"         
##  [4925] "Hnrnpa0"        "Lrrn2"          "Gkap1"          "Kif27"         
##  [4929] "Qng1"           "Mir7-1"         "4921517D22Rik"  "Spata31d1a"    
##  [4933] "Spata31d1d"     "Zfp935"         "Zfp1008"        "Gm7045"        
##  [4937] "Plekha6"        "Platr25"        "Fbp2"           "Fancc"         
##  [4941] "Ptch1"          "Rpl10a"         "Hsd17b3"        "Prxl2c"        
##  [4945] "Ctsl"           "Cntnap3"        "Prss47"         "Ren1"          
##  [4949] "Mfsd14b"        "Zfp640"         "Gm33043"        "BC049692"      
##  [4953] "Mterf3"         "Rslcan18"       "Zfp458"         "Zfp457"        
##  [4957] "Zfp595"         "Zfp953"         "Gm10537"        "Zfp456"        
##  [4961] "Zfp874a"        "Zfp58"          "Zfp87"          "Zfp748"        
##  [4965] "Zfp729b"        "Zfp729a"        "Zfp738"         "Tent4a"        
##  [4969] "Srd5a1"         "Chit1"          "Ice1"           "Irx1"          
##  [4973] "Slc6a18"        "Nkd2"           "Trip13"         "Exoc3"         
##  [4977] "Pdcd6"          "Zfp72"          "Zfp825"         "Cast"          
##  [4981] "Naxe"           "Chi3l1"         "Gm8278"         "Gm3926"        
##  [4985] "Rhobtb3"        "Arsk"           "Fam81b"         "Slf1"          
##  [4989] "Gm5042"         "Gm8345"         "Adgrv1"         "Polr3g"        
##  [4993] "Mybph"          "Gm5666"         "Gm12338"        "Gm8546"        
##  [4997] "Xrcc4"          "Atp6ap1l"       "Atg10"          "4833422C13Rik" 
##  [5001] "Zcchc9"         "Ckmt2"          "Msh3"           "Mgat4f"        
##  [5005] "Zfyve16"        "Thbs4"          "Tent2"          "Jmy"           
##  [5009] "Bhmt"           "Bhmt2"          "Scamp1"         "Pde8b"         
##  [5013] "Aggf1"          "Crhbp"          "Cyb5r1"         "F2r"           
##  [5017] "Iqgap2"         "Sv2c"           "Polk"           "Hexb"          
##  [5021] "Btf3"           "Sec61b"         "Tmem171"        "Fcho2"         
##  [5025] "Tnpo1"          "Adipor1"        "H2bl1"          "Ptcd2"         
##  [5029] "Map1b"          "Cartpt"         "BC001981"       "Gm54974"       
##  [5033] "Gtf2h2"         "Marveld2"       "Rad17"          "Cdk7"          
##  [5037] "Ube2t"          "Mrps36"         "Cenph"          "Slc30a5"       
##  [5041] "Gm6114"         "Pik3r1"         "Srek1"          "Nln"           
##  [5045] "Trappc13"       "Ppwd1"          "Cwc27"          "Gm10535"       
##  [5049] "Rgs7bp"         "Ipo11"          "Kif2a"          "Ndufaf2"       
##  [5053] "Gm30747"        "Gemin8"         "Gapt"           "Gpbp1"         
##  [5057] "Map3k1"         "Gpx8"           "Arl8a"          "Gm41069"       
##  [5061] "Snx18"          "Ndufs4"         "Fst"            "Itga2"         
##  [5065] "Parp8"          "Gm17509"        "Gm5200"         "Mrps30"        
##  [5069] "3110070M22Rik"  "Csrp1"          "Zfp131"         "Nim1k"         
##  [5073] "Gm3500"         "Gm3095"         "Slbp"           "Flnb"          
##  [5077] "Abhd6"          "Rpp14"          "Pxk"            "Kctd6"         
##  [5081] "Phlda3"         "Ptprg"          "Cep15"          "Synpr"         
##  [5085] "Sntn"           "Slc4a7"         "Nek10"          "Ngly1"         
##  [5089] "Top2b"          "Gm7084"         "Nkiras1"        "Cox18"         
##  [5093] "Tnnt2"          "Gm12202"        "Gm8582"         "Nid2"          
##  [5097] "Fam149b"        "1810062O18Rik"  "Sec24c"         "Fut11"         
##  [5101] "Chchd1"         "Vcl"            "Adk"            "Tmem9"         
##  [5105] "Lrmda"          "Cnot1"          "E330034G19Rik"  "Gm18276"       
##  [5109] "Zmiz1"          "Ppif"           "Anxa11"         "4933413J09Rik" 
##  [5113] "Gm24031"        "9930004E17Rik"  "Kif21b"         "Dnah12"        
##  [5117] "Asb14"          "Il17rd"         "Arhgef3"        "Erc2"          
##  [5121] "Lrtm1"          "Actr8"          "Chdh"           "Dcp1a"         
##  [5125] "Tkt"            "Kif14"          "Rft1"           "Sfmbt1"        
##  [5129] "Stimate"        "Pbrm1"          "Nt5dc2"         "Tnnc1"         
##  [5133] "Sema3g"         "Bap1"           "Eaf1"           "Galnt15"       
##  [5137] "Zfp281"         "Oxnad1"         "Parg"           "Ogdhl"         
##  [5141] "Drgx"           "Vstm4"          "Lrrc18"         "Gm6340"        
##  [5145] "Frmpd2"         "Gdf10"          "Gm5460"         "Dennd1b"       
##  [5149] "Antxrl"         "Syt15"          "Glud1"          "Grid1"         
##  [5153] "Mir346"         "4930474N05Rik"  "Gm5203"         "Eif1-ps1"      
##  [5157] "Gm2791"         "Dydc1"          "Zbtb41"         "Sftpa1"        
##  [5161] "Ear2"           "BC061237"       "Bnip3"          "Psmc6"         
##  [5165] "Cdkn3"          "Cgrrf1"         "Socs4"          "Mapk1ip1l"     
##  [5169] "Lgals3"         "Aspm"           "Fbxo34"         "Ktn1"          
##  [5173] "Peli2"          "Tmem260"        "Ap5m1"          "Naa30"         
##  [5177] "Or11g27"        "Parp2"          "Pnp"            "Apex1"         
##  [5181] "Uchl5"          "Rnase4"         "Rnase6"         "Rnase2b"       
##  [5185] "Gm7247"         "Gm5622"         "AY358078"       "Ear7"          
##  [5189] "Mettl17"        "Slc39a2"        "Tppp2"          "Gm5263"        
##  [5193] "Arhgef40"       "Rpgrip1"        "Tox4"           "Or4e2"         
##  [5197] "Trav2"          "Trav3-1"        "Trav8d-1"       "Trav13d-4"     
##  [5201] "Trav4d-4"       "Trav6d-6"       "Ppm1a"          "Brinp3"        
##  [5205] "Trav4-2"        "Trav8-1"        "Trav15-2-dv6-2" "Trav13-5"      
##  [5209] "Trdv2-1"        "Traj57"         "Abhd4"          "Oxa1l"         
##  [5213] "Mmp14"          "Lrp10"          "Tpr"            "Rem2"          
##  [5217] "Gm42368"        "Psmb11"         "4930579G18Rik"  "1700123O20Rik" 
##  [5221] "Rnf212b"        "Bcl2l2"         "Cmtm5"          "Mhrt"          
##  [5225] "Ngdn"           "Niban1"         "Gm10364"        "Carmil3"       
##  [5229] "Cpne6"          "Dcaf11"         "Fitm1"          "Psme1"         
##  [5233] "Rnf31"          "Ltb4r2"         "Ltb4r1"         "Khnyn"         
##  [5237] "Edem3"          "Atp12a"         "2410022M11Rik"  "Ift88"         
##  [5241] "Il17d"          "Sap18"          "Fgf9"           "Rpl13"         
##  [5245] "Rcbtb1"         "Cab39l"         "Shisa2"         "Apobec4"       
##  [5249] "Gm6066"         "Arl11"          "Trim13"         "Rnaseh2b"      
##  [5253] "Fam124a"        "Serpine3"       "Wdfy2"          "Ctsb"          
##  [5257] "Fam167a"        "Xkr6"           "Arpc5"          "Mir598"        
##  [5261] "Pinx1"          "Sox7"           "Prss51"         "Prss52"        
##  [5265] "Kif13b"         "Zfp395"         "Nuggc"          "Scara5"        
##  [5269] "Pbk"            "Nmnat2"         "Ccdc25"         "Clu"           
##  [5273] "Trim35"         "Pnma2"          "Gm9570"         "Kctd9"         
##  [5277] "Gnrh1"          "Nkx2-6"         "Tnfrsf10b"      "Egr3"          
##  [5281] "Shcbp1l"        "Bin3"           "1700031C06Rik"  "Gm9174"        
##  [5285] "Mir320"         "Reep4"          "Hr"             "Nudt18"        
##  [5289] "Dok2"           "Gfra2"          "Rcbtb2"         "Rgs16"         
##  [5293] "Lpar6"          "Med4"           "Esd"            "Gm10847"       
##  [5297] "Zc3h13"         "Siah3"          "Erich6b"        "Snora31"       
##  [5301] "Nufip1"         "4930431P22Rik"  "Stx6"           "Ccdc122"       
##  [5305] "Enox1"          "Epsti1"         "Gm4821"         "Mtrf1"         
##  [5309] "Kbtbd7"         "Elf1"           "Sugt1"          "Pcdh17"        
##  [5313] "Gm9264"         "Atg5"           "Acbd6"          "Tdrd3"         
##  [5317] "Ccdc202"        "Snora30"        "Pibf1"          "Klf5"          
##  [5321] "4930517O19Rik"  "Lmo7"           "Cln5"           "Slain1"        
##  [5325] "Ndfip2"         "Tor1aip2"       "Trim52"         "Frg2f4"        
##  [5329] "Slitrk5"        "Mir17hg"        "Gpc6"           "Dnajc3"        
##  [5333] "Cldn10"         "Hs6st3"         "Rap2a"          "Gm25781"       
##  [5337] "Nphs2"          "Timm8a2"        "Tm9sf2"         "Clybl"         
##  [5341] "Gm10837"        "Pcca"           "4930594M22Rik"  "Itgbl1"        
##  [5345] "4930469B13Rik"  "Fam107a"        "Fam3d"          "Abl2"          
##  [5349] "Cfap20dc"       "Gm43041"        "Ptma"           "Fhit"          
##  [5353] "Rpl19"          "Thoc7"          "Psmd6"          "Gm8483"        
##  [5357] "Oxsm"           "Rarb"           "Pclaf"          "Gm55487"       
##  [5361] "Nr1d2"          "Ube2e2"         "Gng2"           "Saysd1"        
##  [5365] "Kcnk5"          "Ecd"            "Mrps16"         "Cfap70"        
##  [5369] "Mss51"          "Gm34423"        "Ppp3cb"         "Usp54"         
##  [5373] "Synpo2l"        "Ndst2"          "Camk2g"         "Gm6128"        
##  [5377] "Ap3m1"          "Dusp29"         "Comtd1"         "Kcnma1"        
##  [5381] "Astn1"          "Dlg5"           "Gm52995"        "Polr3a"        
##  [5385] "4930542C16Rik"  "Ppifos"         "1700054O19Rik"  "Zcchc24"       
##  [5389] "Plac9"          "Slmap"          "Arf4os"         "Gm31256"       
##  [5393] "Pde12"          "Ccdc66"         "Il17rb"         "Cacna1d"       
##  [5397] "Uqcc5"          "Sh3bp5"         "Hacl1"          "Slc18a3"       
##  [5401] "3425401B19Rik"  "Wdfy4"          "Gm10530"        "Mapk8"         
##  [5405] "Gprin2"         "Shld2"          "Fam25a"         "Sncg"          
##  [5409] "Bmpr1a"         "9230112D13Rik"  "Ldb3"           "Opn4"          
##  [5413] "4930596D02Rik"  "4930523C07Rik"  "Gm7853"         "Ccser2"        
##  [5417] "Rgr"            "Gpr15lg"        "Ghitm"          "Tspan14"       
##  [5421] "Prxl2a"         "Dydc2"          "Ero1a"          "Fermt2"        
##  [5425] "Rragc"          "Mrps14"         "Cnih1"          "Gmfb"          
##  [5429] "Gm10371"        "Wdhd1"          "Dlgap5"         "Atg14"         
##  [5433] "Map1lc3b"       "Exoc5"          "Ccdc198"        "Gm22116"       
##  [5437] "Rpl23a"         "Or4n4"          "Or4n4b"         "Or4m1"         
##  [5441] "Or4q3"          "Ttc5"           "Ccnb1ip1"       "Rpph1"         
##  [5445] "Tep1"           "Osgep"          "Pip4p1"         "Rc3h1"         
##  [5449] "Rnase11"        "Or6s1"          "Rnase1"         "Gm5800"        
##  [5453] "Ndrg2"          "Zfp219"         "Hnrnpc"         "Chd8"          
##  [5457] "Snord8"         "Rab2b"          "Serpinc1"       "Mettl3"        
##  [5461] "Or10g3"         "Or10g1"         "Nrbf2"          "A630038E17Rik" 
##  [5465] "Dad1"           "Prmt5"          "Haus4"          "Ajuba"         
##  [5469] "Psmb5"          "Gas5"           "Cdh24"          "Acin1"         
##  [5473] "Cebpe"          "Slc7a8"         "Homez"          "Ppp1r3e"       
##  [5477] "Slc22a17"       "Efs"            "Myh7"           "Zfhx2"         
##  [5481] "Cenpl"          "Jph4"           "Gm10876"        "A730061H03Rik" 
##  [5485] "Psme2"          "Tm9sf1"         "Mdp1"           "Tinf2"         
##  [5489] "Cideb"          "Sdr39u1"        "Gm5801"         "Ankrd45"       
##  [5493] "Gzmn"           "Cpap"           "Zmym5"          "Gja3"          
##  [5497] "Gjb2"           "Cryl1"          "Ska3"           "Zdhhc20"       
##  [5501] "Micu2"          "1700129C05Rik"  "SLC9C2"         "Gm5142"        
##  [5505] "Phf11c"         "Setdb2"         "Cdadc1"         "Gm47810"       
##  [5509] "Mipepos"        "Tnfrsf19"       "Ebpl"           "Kpna3"         
##  [5513] "Spryd7"         "Gm10176"        "Mir15a"         "Defb30"        
##  [5517] "Fdft1"          "Gata4"          "Mtmr9"          "4930578I06Rik" 
##  [5521] "Hmbox1"         "Extl3"          "Fzd3"           "Pnoc"          
##  [5525] "Vamp4"          "Elp3"           "Esco2"          "Ptk2b"         
##  [5529] "Dpysl2"         "Ppp2r2a"        "Dock5"          "Slc25a37"      
##  [5533] "R3hcc1"         "Chmp7"          "Gm17740"        "Gm29093"       
##  [5537] "Myoc"           "Rhobtb2"        "Ccar2"          "Pdlim2"        
##  [5541] "Sorbs3"         "Ppp3cc"         "Slc39a14"       "Polr3d"        
##  [5545] "Bmp1"           "Fhip2b"         "Dmtn"           "Kifap3"        
##  [5549] "Fgf17"          "Npm2"           "Rb1"            "Lrch1"         
##  [5553] "Lrrc63"         "Cby2"           "Gm25517"        "Gpalpp1"       
##  [5557] "Serp2"          "Fkbp1a-ps1"     "Scyl3"          "Lacc1"         
##  [5561] "Gm1587"         "Dnajc15"        "Tnfsf11"        "Akap11"        
##  [5565] "Naa16"          "Wbp4"           "Cnmd"           "Gm10845"       
##  [5569] "Gm33121"        "Mettl18"        "Rps3a1"         "Pcdh20"        
##  [5573] "Gm7272"         "Gm7232"         "Pcdh9"          "Dach1"         
##  [5577] "Mzt1"           "Klf12"          "Gm9302"         "Tbc1d4"        
##  [5581] "Sele"           "Commd6"         "Gm9922"         "Gm5854"        
##  [5585] "Fbxl3"          "Mycbp2"         "Obi1"           "Rpl27a-ps2"    
##  [5589] "Slitrk1"        "Dct"            "Tgds"           "F5"            
##  [5593] "Sox21"          "Abcc4"          "Dzip1"          "Stk24"         
##  [5597] "Dock9"          "Gm5089"         "Gm9399"         "Tmtc4"         
##  [5601] "Fgf14"          "Selenop"        "Slc19a2"        "Oxct1"         
##  [5605] "Prkaa1"         "Ttc33"          "Dab2"           "C9"            
##  [5609] "Fyb1"           "Rictor"         "Lifr"           "Gdnf"          
##  [5613] "Nup155"         "Ccdc181"        "Cplane1"        "Capsl"         
##  [5617] "Prlr"           "Rad1"           "C1qtnf3"        "Amacr"         
##  [5621] "Zfr"            "Golph3"         "Gm19840"        "Cdh18"         
##  [5625] "Nme7"           "Myo10"          "Retreg1"        "Zfp622"        
##  [5629] "Marchf11"       "Ank"            "Dnah5"          "Ctnnd2"        
##  [5633] "Cmbl"           "Atpsckmt"       "Sema5a"         "Gpr161"        
##  [5637] "Sdc2"           "Cpq"            "Mtdh"           "Laptm4b"       
##  [5641] "Erich5"         "Osr2"           "Gm18994"        "Gm22979"       
##  [5645] "Polr2k"         "Spag1"          "Mir8101"        "Mpc2"          
##  [5649] "Grhl2"          "Cthrc1"         "Dcaf13"         "Zfpm2"         
##  [5653] "Emc2"           "Gm2140"         "Eny2"           "Pkhd1l1"       
##  [5657] "Ebag9"          "A930017M01Rik"  "Adcy10"         "4930548G14Rik" 
##  [5661] "Aard"           "Med30"          "Gm7489"         "Colec10"       
##  [5665] "Ccn3"           "Deptor"         "Col14a1"        "Mtbp"          
##  [5669] "Zhx2"           "Creg1"          "Tbc1d31"        "Fam83a"        
##  [5673] "Ntaq1"          "Trmt12"         "Ndufb9"         "Gm7691"        
##  [5677] "Sqle"           "Nsmce2"         "Tsg101"         "Gsdmcl-ps"     
##  [5681] "Cd247"          "Efr3a"          "Phf20l1"        "Ccn4"          
##  [5685] "Gm41341"        "Khdrbs3"        "Chrac1"         "Ptp4a3"        
##  [5689] "Gm22106"        "Adgrb1"         "4933427E11Rik"  "Gpa33"         
##  [5693] "Psca"           "Them6"          "Gml2"           "Ly6e"          
##  [5697] "Ly6f"           "Gpihbp1"        "Zfp41"          "Gm38506"       
##  [5701] "Rhpn1"          "Tigd5"          "Ildr2"          "Zfp707"        
##  [5705] "Mapk15"         "Spatc1"         "Smpd5"          "Exosc4"        
##  [5709] "Gpaa1"          "Cyc1"           "Maf1"           "Wdr97"         
##  [5713] "Hgh1"           "Aldh9a1"        "Mroh1"          "Hsf1"          
##  [5717] "Adck5"          "Kifc2"          "Ppp1r16a"       "Lrrc14"        
##  [5721] "Commd5"         "Rpl8"           "1110038F14Rik"  "Apol10a"       
##  [5725] "Lmx1a"          "Csf2rb"         "Kctd17"         "1700041B01Rik" 
##  [5729] "Gga1"           "Sh3bp1"         "Lgals1"         "Triobp"        
##  [5733] "H1f0"           "Galr3"          "Eif3l"          "Rgs5"          
##  [5737] "Pick1"          "Maff"           "Cby1"           "Tomm22"        
##  [5741] "Gtpbp1"         "Gm55311"        "Apobec3"        "Syngr1"        
##  [5745] "Mgat3"          "Mief1"          "4930500M09Rik"  "Cacna1i"       
##  [5749] "Adsl"           "4930483J18Rik"  "Mchr1"          "Xpnpep3"       
##  [5753] "Rbx1"           "Ep300"          "Zc3h7b"         "Aco2"          
##  [5757] "Csdc2"          "Ddb1"           "Spata46"        "Gm5805"        
##  [5761] "Ndufb11b"       "Xrcc6"          "4930407I10Rik"  "Mei1"          
##  [5765] "Ccdc134"        "Smim45"         "Smdt1"          "Gm54394"       
##  [5769] "Cyp2d9"         "Gm7299"         "Rnu12"          "Bik"           
##  [5773] "Tspo"           "Mpped1"         "Pnpla3"         "Samm50"        
##  [5777] "Parvb"          "Prr5"           "Arhgap8"        "Nup50"         
##  [5781] "Olfml2b"        "Upk3a"          "Fam118a"        "Ribc2"         
##  [5785] "Ppara"          "Ttc38"          "Gramd4"         "Tbc1d22a"      
##  [5789] "Tafa5"          "Creld2"         "Gm33049"        "Gm9929"        
##  [5793] "Mov10l1"        "Panx2"          "Trabd"          "Selenoo"       
##  [5797] "Ppp6r2"         "Ncaph2"         "C730034F03Rik"  "Mapk8ip2"      
##  [5801] "Acr"            "Gm3861"         "Gm26620"        "Lrrk2"         
##  [5805] "Irak4"          "Tmem117"        "Ano6"           "Pced1b"        
##  [5809] "Slc48a1"        "Pfkm"           "Ccdc184"        "1700031M16Rik" 
##  [5813] "Or8s10"         "Cfap126"        "Or5bs2"         "Or11m3"        
##  [5817] "9330020H09Rik"  "Spmip11"        "Cacnb3"         "Ccdc65"        
##  [5821] "B130046B21Rik"  "Rpl36"          "Troap"          "Prpf40b"       
##  [5825] "Mpz"            "Tmbim6"         "Aqp2"           "Aqp5"          
##  [5829] "Asic1"          "Smarcd1"        "Cox14"          "Larp4"         
##  [5833] "Tmprss12"       "Tmt1a"          "Letmd1"         "Apoa2"         
##  [5837] "Dazap2"         "Scn8a"          "Eif4b"          "Igfbp6"        
##  [5841] "Gm9918"         "Mfsd5"          "Espl1"          "Pfdn5"         
##  [5845] "Myg1"           "Map3k12"        "B4galt3"        "Tarbp2"        
##  [5849] "Hoxc9"          "Hoxc8"          "Mir615"         "Gm10830"       
##  [5853] "Copz1"          "Nckap1l"        "Gm7962"         "Ghr"           
##  [5857] "Gm4823"         "Nectin4"        "C7"             "Card6"         
##  [5861] "Atp5pd"         "Osmr"           "Egflam"         "Slc1a3"        
##  [5865] "Gm5210"         "Spef2"          "Dnajc21"        "Brix1"         
##  [5869] "Gm47260"        "1700037C18Rik"  "Arhgap30"       "Ttc23l"        
##  [5873] "Gm8174"         "Rai14"          "Tars1"          "Npr3"          
##  [5877] "Pdzd2"          "6030458C11Rik"  "Cdh6"           "Gm8328"        
##  [5881] "Gm8341"         "Usf1"           "Acot10"         "Basp1"         
##  [5885] "Fbxl7"          "Otulin"         "Trio"           "Gm26163"       
##  [5889] "Ankrd33b"       "Ropn1l"         "Ube2v2"         "Marchf6"       
##  [5893] "F11r"           "Cct5"           "Rpl30"          "Rida"          
##  [5897] "Stk3"           "Cox6c"          "Fbxo43"         "Ywhaz"         
##  [5901] "Zfp706"         "Gm9509"         "Gm8664"         "Alyref2"       
##  [5905] "Ncald"          "Gm8705"         "Klf10"          "G930009F23Rik" 
##  [5909] "Slc25a32"       "Eif3e"          "Nudcd1"         "Sybu"          
##  [5913] "Gm5471"         "Gm5472"         "Cd48"           "Csmd3"         
##  [5917] "Eif3h"          "Ext1"           "Samd12"         "Tnfrsf11b"     
##  [5921] "Enpp2"          "Taf2"           "Dscc1"          "Mrpl13"        
##  [5925] "Sntb1"          "Tma7"           "9130401M01Rik"  "Tmem65"        
##  [5929] "Ube2d4"         "Tatdn1"         "Mtss1"          "4933412E24Rik" 
##  [5933] "Gm24696"        "Macroh2a3"      "Gm25702"        "Gm4942"        
##  [5937] "Pex19"          "Gsdmc2"         "Cyrib"          "Asap1"         
##  [5941] "Oc90"           "Hhla1"          "Kcnq3"          "Ndrg1"         
##  [5945] "Zfat"           "Mir30d"         "Gm7859"         "Pigm"          
##  [5949] "Fam135b"        "Trappc9"        "Ago2"           "Gpr20"         
##  [5953] "Mroh5"          "Sf3b4"          "Arc"            "Jrk"           
##  [5957] "Slurp1"         "Slurp2"         "Slamf9"         "Ly6d"          
##  [5961] "Ly6g6g"         "Ly6k"           "Gml"            "Cyp11b1"       
##  [5965] "Cyp11b2"        "Ly6m"           "Ly6a"           "Top1mt"        
##  [5969] "Mafa"           "Igsf9"          "Naprt"          "Eef1d"         
##  [5973] "Gfus"           "Ccdc166"        "Eppk1"          "Plec"          
##  [5977] "Parp10"         "Mirt2"          "Oplah"          "Tssk5"         
##  [5981] "Snapin"         "Tagln2"         "Rpl29"          "Tmem249"       
##  [5985] "Fbxl6"          "Cpsf1"          "Slc39a4"        "Tonsl"         
##  [5989] "Lrrc24"         "Arhgap39"       "Zfp251"         "Mb"            
##  [5993] "Cfap45"         "Apol8"          "Myh9"           "Txn2"          
##  [5997] "Eif3d"          "Cacng2"         "Ift27"          "Csf2rb2"       
##  [6001] "Cimip4"         "Tst"            "Tmprss6"        "Vsig8"         
##  [6005] "C1qtnf6"        "Elfn2"          "Card10"         "Ankrd54"       
##  [6009] "Sox10"          "Slc16a8"        "Baiap2l2"       "Pla2g6"        
##  [6013] "Tmem184b"       "Csnk1e"         "Crp"            "Ddx17"         
##  [6017] "Dmc1"           "Josd1"          "Sun2"           "Dnal4"         
##  [6021] "D730005E14Rik"  "Cbx7"           "Pdgfb"          "Enthd1"        
##  [6025] "Mrtfa"          "Or10j5"         "Slc25a17"       "St13"          
##  [6029] "Dnajb7"         "Tob2"           "Phf5a"          "Polr3h"        
##  [6033] "Pmm1"           "Snu13"          "Tnfrsf13c"      "Cenpm"         
##  [6037] "Or6n2"          "Naga"           "Ndufa6"         "Cyp2d22"       
##  [6041] "Cyp2d10"        "Cyp2d37-ps"     "Cyp2d40"        "Cyp2d41-ps"    
##  [6045] "Cyp2d26"        "Tbrg3"          "Rrp7a"          "Spta1"         
##  [6049] "Cyb5r3"         "Vkorc1l1"       "Ttll1"          "Mcat"          
##  [6053] "Ttll12"         "Scube1"         "Efcab6"         "Sult4a1"       
##  [6057] "Gm5214"         "Phf21b"         "Or6p1"          "5031439G07Rik" 
##  [6061] "Smc1b"          "Pkdrej"         "Cerk"           "Alg12"         
##  [6065] "Mlc1"           "Hdac10"         "Plxnb2"         "Dennd6b"       
##  [6069] "Sbf1"           "Exo1"           "Lmf2"           "Cimap1b"       
##  [6073] "Arsa"           "Rabl2"          "Cpne8"          "Kif21a"        
##  [6077] "Abcd2"          "Slc2a13"        "Gxylt1"         "Zcrb1"         
##  [6081] "Sdccag8"        "Prickle1"       "Adamts20"       "Pus7l"         
##  [6085] "Twf1"           "Nell2"          "Scaf11"         "Slc38a1"       
##  [6089] "Slc38a2"        "Gm8888"         "Amigo2"         "Atox1"         
##  [6093] "Spmip3"         "Hdac7"          "Vdr"            "Col2a1"        
##  [6097] "Asb8"           "Zfp641"         "Or8s5"          "Kansl2"        
##  [6101] "Ccnt1"          "Ddx23"          "Arf3"           "Catspere2"     
##  [6105] "Wnt10b"         "Kmt2d"          "Lmbr1l"         "Tuba1a"        
##  [6109] "C1ql4"          "Mcrs1"          "Fam186b"        "Gm22951"       
##  [6113] "Nckap5l"        "Racgap1"        "Desi2"          "Lima1"         
##  [6117] "Fam186a"        "2310068J16Rik"  "Slc11a2"        "Csrnp2"        
##  [6121] "Tfcp2"          "Smagp"          "Bin2"           "Krt87"         
##  [6125] "Krt82"          "Cox20"          "Krt75"          "Gm5414"        
##  [6129] "Krt6b"          "Krt5"           "Krt73"          "Krt1"          
##  [6133] "Krt77"          "Krt79"          "Krt8"           "Csad"          
##  [6137] "Gm24405"        "Npff"           "Atf7"           "Mir688"        
##  [6141] "Calcoco1"       "Cbx5"           "Zfp385a"        "Gtsf1"         
##  [6145] "Gtsf2"          "Gm9108"         "Or1f19"         "Cnst"          
##  [6149] "Zfp263"         "Gm54882"        "Zfp174"         "Cluap1"        
##  [6153] "Vasn"           "Hmox2"          "4930562C15Rik"  "Mgrn1"         
##  [6157] "Dnaaf8"         "Ubn1"           "Gm10518"        "Sec14l5"       
##  [6161] "Mettl22"        "Pmm2"           "Gm7572"         "Rpl39l"        
##  [6165] "Atf7ip2"        "Nubp1"          "Clec16a"        "Snn"           
##  [6169] "Snx29"          "Cdc42bpa"       "Gm9961"         "Shisa9"        
##  [6173] "Ercc4"          "Mrtfb"          "Mir365-1"       "Bfar"          
##  [6177] "Ntan1"          "Mpv17l"         "Bmerb1"         "Mir484"        
##  [6181] "Itpkb"          "Nde1"           "Gm1758"         "A630010A05Rik" 
##  [6185] "Snai2"          "Clxn"           "Prkdc"          "Pkp2"          
##  [6189] "Yars2"          "Ppm1f"          "Gm6438"         "Parp1"         
##  [6193] "Ydjc"           "Hic2"           "Serpind1"       "Snap29"        
##  [6197] "Aifm3"          "Lztr1"          "P2rx6"          "Smpd4"         
##  [6201] "Ccdc74a"        "Scarf2"         "Snrnp27"        "Lin9"          
##  [6205] "Fam246a"        "Tssk1"          "Tssk2"          "Vpreb1b"       
##  [6209] "Gm49580"        "Dgcr6"          "Rtn4r"          "Trmt2a"        
##  [6213] "Gnb1l"          "4930588K23Rik"  "H3f3aos"        "Gm10088"       
##  [6217] "Gm17799"        "Yeats2"         "Eif2b5"         "Dvl3"          
##  [6221] "Ap2m1"          "Abcf3"          "Polr2h"         "Chrd"          
##  [6225] "Gm9697"         "Sde2"           "Map3k13"        "Ndufa11"       
##  [6229] "Gm26980"        "Dnajb11"        "Fetub"          "St6gal1"       
##  [6233] "Rtp1"           "Rtp4"           "Lpp"            "Mir28a"        
##  [6237] "Pycr2"          "Trp63"          "Ccdc50"         "Hes1"          
##  [6241] "1700025H01Rik"  "Bdh1"           "Meltf"          "Ncbp2"         
##  [6245] "Cep19"          "Smco1"          "Ubxn7"          "Cnih4"         
##  [6249] "Dynlt2b"        "Pcyt1a"         "Zdhhc19"        "Tfrc"          
##  [6253] "Tnk2"           "Muc4"           "Lmln"           "Snx4"          
##  [6257] "Heg1"           "Itgb5"          "Srp9"           "Ropn1"         
##  [6261] "Mylk"           "Hacd2"          "Kpna1"          "Wdr5b"         
##  [6265] "Mix23"          "Ildr1"          "Iqcb1"          "Golgb1"        
##  [6269] "Hcls1"          "Trp53bp2"       "Rabl3"          "Fstl1"         
##  [6273] "Lrrc58"         "Gpr156"         "Cox17"          "Popdc2"        
##  [6277] "Tmem39a"        "Igsf11"         "Zbtb20"         "Ccdc191"       
##  [6281] "Capn8"          "Naa50"          "Usf3"           "Spice1"        
##  [6285] "Nepro"          "Ccdc80"         "Atg3"           "Gm5406"        
##  [6289] "Slc9c1"         "Gm6912"         "Gm7275"         "Rab3gap2"      
##  [6293] "Gm17804"        "Prdx1"          "Morc1"          "Myh15"         
##  [6297] "Ift57"          "Cd47"           "Gm8824"         "1700116B05Rik" 
##  [6301] "Cblb"           "Rpl24"          "Mir194-1"       "Zbtb11"        
##  [6305] "Senp7"          "Abi3bp"         "Tomm70a"        "Filip1l"       
##  [6309] "Dcbld2"         "Cpox"           "Cldnd1"         "Gabrr3"        
##  [6313] "Orai2"          "Gm23645"        "Bpnt1"          "Riox2"         
##  [6317] "Sinhcaf"        "Gm25986"        "Pros1"          "Vgll3"         
##  [6321] "4933411O13Rik"  "Gbe1"           "Robo1"          "Rbm11"         
##  [6325] "Mir99ahg"       "Eprs1"          "Gm21816"        "Mir99a"        
##  [6329] "Mirlet7c-1"     "Cxadr"          "Fkbp1a-ps3"     "Jam2"          
##  [6333] "Gabpa"          "Gm10791"        "N6amt1"         "Usp16"         
##  [6337] "Slc30a10"       "Map3k7cl"       "Bach1"          "Krtap13-23"    
##  [6341] "krtap20-23"     "Krtap20-20"     "Gm2805"         "Sod1"          
##  [6345] "Hunk"           "1110008E08Rik"  "Mrap"           "Gm26169"       
##  [6349] "Eva1c"          "Olig1"          "Ifnar2"         "Il10rb"        
##  [6353] "Ifnar1"         "Ifngr2"         "Gm10785"        "Slc5a3"        
##  [6357] "Kcne2"          "Smim11"         "Gm3809"         "Cbr1"          
##  [6361] "Dop1b"          "Morc3"          "Chaf1b"         "Dyrk1a"        
##  [6365] "Ets2"           "1700093J21Rik"  "Get1"           "Igsf5"         
##  [6369] "B230307C23Rik"  "Ush2a"          "Zfp597"         "Crebbp"        
##  [6373] "Adcy9"          "Srl"            "Pam16"          "Coro7"         
##  [6377] "Anks3"          "Nagpa"          "AU021092"       "Gm55020"       
##  [6381] "Ptpn14"         "Tmem114"        "Tmem186"        "Carhsp1"       
##  [6385] "Emp2"           "Tvp23a"         "Dexi"           "Tnp2"          
##  [6389] "Prm3"           "Prm1"           "Litaf"          "A230020J21Rik" 
##  [6393] "Zc3h7a"         "Gm24145"        "Rsl1d1"         "Gspt1"         
##  [6397] "Cpped1"         "Gm6332"         "2310015D24Rik"  "Parn"          
##  [6401] "Pla2g10"        "Ifitm7"         "Spata45"        "Myh11"         
##  [6405] "Cep20"          "Gm7731"         "Mzt2"           "Dnm1l"         
##  [6409] "Fgd4"           "Or7a40"         "4933404G15Rik"  "Vpreb1a"       
##  [6413] "Gm9974"         "Nsl1"           "Ppil2"          "Mir130b"       
##  [6417] "Thap7"          "Med15"          "Car15"          "Ess2"          
##  [6421] "Gsc2"           "Slc25a1"        "Prodh"          "4933432I09Rik" 
##  [6425] "Gm15573"        "Batf3"          "Ranbp1"         "Dgcr8"         
##  [6429] "Mir185"         "Comt"           "Tbx1"           "Cdc45"         
##  [6433] "Mrpl40"         "Iglv1"          "Map6d1"         "Abcc5"         
##  [6437] "D730003I15Rik"  "Gm15760"        "Alg3"           "Clcn2"         
##  [6441] "Rps10"          "Magef1"         "2510009E07Rik"  "Tmem41a"       
##  [6445] "Tra2b"          "Crygs"          "Tbccd1"         "Pacc1"         
##  [6449] "Rfc4"           "BC106179"       "Gm6640"         "Sst"           
##  [6453] "P3h2"           "Fgf12"          "Mb21d2"         "Lrrc15"        
##  [6457] "Tmem44"         "Lsg1"           "Nek2"           "Ncbp2as2"      
##  [6461] "Pigx"           "Iqcg"           "Umps"           "Sec22a"        
##  [6465] "Gm5963"         "Fam162a"        "Casr"           "Eaf2"          
##  [6469] "Fbxo40"         "Rd3"            "Stxbp5l"        "Pla1a"         
##  [6473] "Adprh"          "Timmdc1"        "Poglut1"        "Arhgap31"      
##  [6477] "Gm15575"        "Upk1b"          "Tex55"          "4932412D23Rik" 
##  [6481] "Gm10516"        "Tigit"          "Qtrt2"          "Zdhhc23"       
##  [6485] "Atp6v1a"        "Sidt1"          "Gtpbp8"         "Slc35a5"       
##  [6489] "Cd200"          "Cd200l1"        "Tagln3"         "Kcnh1"         
##  [6493] "Abhd10"         "Phldb2"         "Plcxd2"         "Cd96"          
##  [6497] "Dzip3"          "Gm22576"        "Gm5407"         "Gm4802"        
##  [6501] "Ccdc54"         "Psmc1"          "Irf6"           "Gm6767"        
##  [6505] "Nfkbiz"         "Nxpe3"          "Cep97"          "Zbtb11os1"     
##  [6509] "Pcnp"           "Trmt10c"        "Adgrg7"         "Tmem45a"       
##  [6513] "Tmem45a2"       "A130010J15Rik"  "Nit2"           "Tbc1d23"       
##  [6517] "Tmem30c"        "Cmss1"          "St3gal6"        "Ftdc2"         
##  [6521] "Gpr15"          "Or5k1"          "Or5ac20"        "Arl6"          
##  [6525] "Plxna2"         "Nsun3"          "Arl13b"         "Epha3"         
##  [6529] "Csnk2a2ip"      "Zfp654"         "Gm16385"        "Htr1f"         
##  [6533] "Chmp2b"         "Cadm2"          "Speer2"         "Tomm5"         
##  [6537] "Cd34"           "Lipi"           "Hspa13"         "Nrip1"         
##  [6541] "Gm7334"         "D16Ertd472e"    "Rps19-ps12"     "Gm54838"       
##  [6545] "Rpl21"          "Gm6032"         "Mrpl39"         "A330023F24Rik" 
##  [6549] "Atp5pf"         "App"            "Cyyr1"          "Adamts1"       
##  [6553] "Adamts5"        "Ltn1"           "Cct8"           "Rpl31-ps4"     
##  [6557] "Krtap19-2"      "Krtap19-4"      "Xkr4"           "Krtap19-9a"    
##  [6561] "Krtap16-3"      "Gm41515"        "Krtap6-5"       "Krtap8-1"      
##  [6565] "Krtap11-1"      "Tiam1"          "Mis18a"         "Cfap298"       
##  [6569] "Synj1"          "Sox17"          "Paxbp1"         "Epcip"         
##  [6573] "H3f3a-ps2"      "Gm9881"         "Dnajc28"        "Atp5po"        
##  [6577] "Fam243"         "Rcan1"          "Cldn14"         "Hlcs"          
##  [6581] "Gm6085"         "Pigp"           "Kcnj6"          "Psmg1"         
##  [6585] "Hmgn1"          "Lca5l"          "Itgb2l"         "Fam3b"         
##  [6589] "Prdm15"         "A630089N07Rik"  "Scaf8"          "Mrpl15"        
##  [6593] "Cldn20"         "Arid1b"         "Gtf2h5"         "Tulp4"         
##  [6597] "Tmem181a"       "Gm1604b"        "Cep43"          "Mpc1"          
##  [6601] "T2"             "T"              "Hmgb3"          "Prkn"          
##  [6605] "Agpat4"         "Gm6618"         "Airn"           "Snora20"       
##  [6609] "Gm10512"        "Smok2a"         "Smok2b"         "Gm7168"        
##  [6613] "Smoc2"          "4732440D04Rik"  "Gm49720"        "Ermard"        
##  [6617] "Chd1"           "BC002059"       "Gm6712"         "Riok2"         
##  [6621] "Spaca6"         "Gm49753"        "Vmn1r224"       "Gm5145"        
##  [6625] "Gm19026"        "Ppp2r1a"        "Zfp160"         "Vmn1r234"      
##  [6629] "Zfp54"          "Zfp51"          "Zfp948"         "Gm31758"       
##  [6633] "Zfp943"         "Zfp758"         "Zfp946"         "Gm54704"       
##  [6637] "Gm9805"         "Gm7898"         "Zscan10"        "Bicdl2"        
##  [6641] "Hcfc1r1"        "Srrm2"          "Prss32"         "Prss21"        
##  [6645] "Dcpp1"          "Dcpp3"          "Tmem129"        "Rnf7"          
##  [6649] "Prss27"         "BC028777"       "Abca3"          "Eci1"          
##  [6653] "Pgp"            "Bricd5"         "Zfp598"         "Noxo1"         
##  [6657] "Rps2"           "Hs3st6"         "Mybl1"          "Meiob"         
##  [6661] "Hagh"           "Igfals"         "Spsb3"          "Mrps34"        
##  [6665] "Nme3"           "Ift140"         "Clcn7"          "Ccdc154"       
##  [6669] "Uqcc4"          "Ppp1r42"        "Tsr3"           "Tpsg1"         
##  [6673] "Tekt4"          "Lmf1"           "Gng13"          "Rpusd1"        
##  [6677] "Ciao3"          "Fbxl16"         "Wdr24"          "Jmjd8"         
##  [6681] "Cops5"          "Mettl26"        "Cox7c"          "Pgap6"         
##  [6685] "Axin1"          "Luc7l"          "Neurl1b"        "Atp6v0e"       
##  [6689] "Bnip1"          "Syngap1"        "Ggnbp1"         "Cpa6"          
##  [6693] "Itpr3"          "Gm10505"        "Hmga1"          "C130040N14Rik" 
##  [6697] "Pacsin1"        "Snrpc"          "Scube3"         "Zfp523"        
##  [6701] "Def6"           "E230001N04Rik"  "Tram1"          "Armc12"        
##  [6705] "Clpsl2"         "Mapk14"         "Mapk13"         "Srsf3"         
##  [6709] "Cdkn1a"         "BC004004"       "Fgd2"           "Pim1"          
##  [6713] "Tbc1d22b"       "Lactb2"         "Rnf8"           "Cmtr1"         
##  [6717] "Umodl1"         "Abcg1"          "Ndufv3"         "4833413E03Rik" 
##  [6721] "Cryaa"          "Rrp1b"          "A530088E08Rik"  "Cyp4f37"       
##  [6725] "Eya1"           "Cyp4f15"        "Zfp952"         "Zfp563"        
##  [6729] "Myo1f"          "Zfp414"         "Kank3"          "Ndufa7"        
##  [6733] "Daxx"           "Zbtb22"         "Tapbp"          "Stau2"         
##  [6737] "Rgl2"           "Wdr46"          "Vps52"          "Rxrb"          
##  [6741] "Col11a2"        "H2-Oa"          "H2-DMb2"        "Tap1"          
##  [6745] "Tap2"           "H2-Ab1"         "Idi1-ps5"       "H2-Eb1"        
##  [6749] "Btnl2"          "Notch4"         "Gpsm3"          "Ager"          
##  [6753] "Atf6b"          "Tnxb"           "Nelfe"          "Ehmt2"         
##  [6757] "Neu1"           "Anapc1"         "Gm5828"         "Hspa1l"        
##  [6761] "Vars1"          "Clic1"          "Ly6g6c"         "Ly6g6e"        
##  [6765] "D17H6S53E"      "Atp6v1g2"       "H2-D1"          "H2-Q1"         
##  [6769] "H2-Q2"          "Gm49089"        "H2-Q3"          "H2-Q4"         
##  [6773] "H2-Q5"          "H2-Q6"          "Cchcr1"         "Psors1c2"      
##  [6777] "Cdsn"           "Flot1"          "Nrm"            "Ppp1r18"       
##  [6781] "Jph1"           "Dhx16"          "Gnl1"           "Gm6034"        
##  [6785] "Gm19684"        "Gm6623"         "Gm8868"         "Trim26"        
##  [6789] "Polr1has"       "Zfp57"          "Gabbr1"         "Gm6075"        
##  [6793] "Gm4831"         "Or14j6"         "Mmut"           "Ldha-ps3"      
##  [6797] "Ptchd4"         "Tnfrsf21"       "Adgrf5"         "Rcan2"         
##  [6801] "Enpp5"          "Runx2os1"       "Gm28341"        "Supt3"         
##  [6805] "B230354K17Rik"  "Aars2"          "Slc35b2"        "Gm25008"       
##  [6809] "Mrpl14"         "Mrps18a"        "Yipf3"          "Lrrc73"        
##  [6813] "Dlk2"           "Mcm3"           "Gm55801"        "Crip3"         
##  [6817] "Mrpl2"          "Cul7"           "Pex6"           "Pex39"         
##  [6821] "Tbcc"           "Mrps10"         "Mrfap1"         "Med20"         
##  [6825] "Tram2"          "Usp49"          "Tfeb"           "1700067P10Rik" 
##  [6829] "Trem6l"         "Trem2"          "Treml1"         "Oard1"         
##  [6833] "Unc5cl"         "Lrfn2"          "Kif6"           "Gm5696"        
##  [6837] "AY702103"       "Plcl2"          "Gm9210"         "Erh"           
##  [6841] "Kat2b"          "4932415M13Rik"  "Gm4471"         "Zfp959"        
##  [6845] "Yju2"           "Shd"            "Rims1"          "Fsd1"          
##  [6849] "Mpnd"           "Chaf1a"         "Hdgfl2"         "A230051N06Rik" 
##  [6853] "Mir7b"          "Safb"           "Catsperd"       "Ranbp3"        
##  [6857] "Dus3l"          "Ppp1r14bl"      "Acsbg3"         "Clpp"          
##  [6861] "Alkbh7"         "Gm17949"        "Trip10"         "Cntnap5c"      
##  [6865] "Nudt12os"       "Fer"            "Gm4701"         "Gm23264"       
##  [6869] "Trappc4"        "Gm6420"         "Ddx11"          "L3mbtl4"       
##  [6873] "Zbtb14"         "Gm9598"         "Dlgap1"         "Gm16519"       
##  [6877] "Gm49905"        "Spdya"          "Wdr43"          "Lbh"           
##  [6881] "Smap1"          "Lclat1"         "Ehd3"           "Spast"         
##  [6885] "Slc30a6"        "Birc6"          "Ltbp1"          "Gm9360"        
##  [6889] "Crim1"          "Gm18649"        "Gpatch11"       "Sdhaf4"        
##  [6893] "Cebpzos"        "Qpct"           "Rmdn2"          "Ttc39d"        
##  [6897] "Gemin6"         "Morn2"          "Tmem178"        "Gm6594"        
##  [6901] "Pkdcc"          "Mta3"           "Spata31e5"      "Dync2li1"      
##  [6905] "Abcg8"          "Camkmt"         "Six3"           "Prkce"         
##  [6909] "Epas1"          "Cript"          "Socs5"          "Ttc7"          
##  [6913] "Msh2"           "Gm5697"         "Rpl36-ps4"      "Gm50040"       
##  [6917] "Gm4832"         "Foxn2"          "Ppp1r21"        "Gm38460"       
##  [6921] "Gtf2a1l"        "Nanp"           "Pja2"           "Pisd-ps2"      
##  [6925] "Gm9898"         "Tfb1m"          "Ldhal6b"        "Gm8363"        
##  [6929] "Serac1"         "Fbl"            "Ftl1"           "Ezr"           
##  [6933] "Mir692-1"       "Gpr31b"         "6530411M01Rik"  "Phf3"          
##  [6937] "Qki"            "Map3k4"         "Slc22a1"        "Igf2r"         
##  [6941] "Mas1"           "Pnldc1"         "Mrpl18"         "Acat3"         
##  [6945] "Acat2"          "Tcte2"          "Alyreffm1"      "4930474M22Rik" 
##  [6949] "Wdr27"          "Phf10"          "Gm7423"         "Psmb1"         
##  [6953] "Gm7177"         "Prdm9"          "Gm6686"         "Rgmb"          
##  [6957] "Oaz1-ps"        "Prim2"          "Lnpep"          "Gm7535"        
##  [6961] "Gm49963"        "Vmn2r109"       "Zfp820"         "Gm6540"        
##  [6965] "Zfp942"         "Gm9514"         "Zfp944"         "Gm16386"       
##  [6969] "Bag2"           "Zfp945"         "Casp16"         "Zfp213"        
##  [6973] "Zfp13"          "Thoc6"          "Tnfrsf12a"      "Cldn9"         
##  [6977] "Paqr4"          "Flywch1"        "Flywch2"        "Psmc5"         
##  [6981] "Pfdn6"          "Gm15455"        "Prss33"         "Prss41"        
##  [6985] "Sbpl"           "Prss22"         "Kctd5"          "Amdhd2"        
##  [6989] "Tbc1d24"        "Ccnf"           "D330041H03Rik"  "E4f1"          
##  [6993] "Bend6"          "Mlst8"          "Traf7"          "Tsc2"          
##  [6997] "Npw"            "Gfer"           "Ndufb10"        "Fahd1"         
##  [7001] "Nubp2"          "Eme2"           "Jpt2"           "Ccdc115"       
##  [7005] "Cramp1"         "Gnptg"          "Baiap3"         "Ube2i"         
##  [7009] "Tpsab1"         "Cacna1h"        "Sox8"           "Chtf18"        
##  [7013] "Gm55306"        "Metrn"          "Prss40"         "Stub1"         
##  [7017] "Wdr90"          "Mcrip2"         "Wfikkn1"        "Rab40c"        
##  [7021] "Pigq"           "Rab11fip3"      "Arhgdig"        "Fam234a"       
##  [7025] "Dusp1"          "Fam168b"        "Nkx2-5"         "Itpr3os"       
##  [7029] "Uqcc2"          "Smim29"         "Spdef"          "Taf11"         
##  [7033] "Tead3"          "Tulp1"          "Fkbp5"          "Clps"          
##  [7037] "Uggt1"          "Srpk1"          "Bnip5"          "Pxt1"          
##  [7041] "Stk38"          "Trp53cor1"      "Cpne5"          "Ppil1"         
##  [7045] "Mtch1"          "Tmem217b"       "Tmem217"        "Lman2l"        
##  [7049] "Ccdc167"        "Mdga1"          "Gm9937"         "Tff3"          
##  [7053] "Tff1"           "Tmprss3"        "Rsph1"          "U2af1"         
##  [7057] "Sik1"           "Hsf2bp"         "Ankrd39"        "Notch3"        
##  [7061] "Akap8"          "Akap8l"         "Wiz"            "Zfp871"        
##  [7065] "Gm7059"         "Zfp870"         "Cyp4f41-ps"     "Zfp763"        
##  [7069] "Phf8l"          "Sema4c"         "Morc2b"         "Zfp81"         
##  [7073] "Zfp101"         "Hnrnpm"         "Rab11b"         "Angptl4"       
##  [7077] "H2-K2"          "H2-K1"          "Mir219a-1"      "Hsd17b8"       
##  [7081] "Fam178b"        "Slc39a7"        "H2-Aa"          "Btnl5-ps"      
##  [7085] "Rnf5"           "Egfl8"          "C4b"            "C4a"           
##  [7089] "Skic2"          "C2"             "Hspa1a"         "Ilf2"          
##  [7093] "Actr1b"         "Gm10501"        "D17H6S56E-5"    "Msh5"          
##  [7097] "Mpig6b"         "Ly6g6f"         "Gm23442"        "Lst1"          
##  [7101] "Tcf19"          "Muc21"          "Vars2"          "F830112A20Rik" 
##  [7105] "Gtf2h4"         "Tubb5"          "Ppp1r18os"      "2310061I04Rik" 
##  [7109] "Atat1"          "Abcf1"          "H2-T23"         "H2-T22"        
##  [7113] "H2-T10"         "Gm20545"        "Gm32899"        "Rpp21"         
##  [7117] "Ppp1r11"        "Polr1h"         "Or2h1"          "Or10c1"        
##  [7121] "Gm25104"        "Or14j9"         "Or2j3"          "AY036118"      
##  [7125] "Pgk2"           "Mgat4a"         "Cenpq"          "Cd2ap"         
##  [7129] "Slc25a27"       "Runx2"          "4930564C03Rik"  "Gm4766"        
##  [7133] "Tmem151b"       "Hsp90ab1"       "Mymx"           "Capn11"        
##  [7137] "Cracdl"         "Tmem63b"        "Vegfa"          "Rsph9"         
##  [7141] "Mad2l1bp"       "Polr1c"         "Tjap1"          "Ttbk1"         
##  [7145] "Cul9"           "Srf"            "Ptk7"           "Tsga10"        
##  [7149] "Klc4"           "Gnmt"           "Cnpy3"          "Ptcra"         
##  [7153] "Bicral"         "Gm16494"        "Taf8"           "Bysl"          
##  [7157] "Tomm6"          "Mdfi"           "Txndc9"         "Gm25201"       
##  [7161] "Foxp4"          "1700122O11Rik"  "9830107B12Rik"  "A530064D06Rik" 
##  [7165] "Nfya"           "Dazl"           "Tbc1d5"         "Kcnh8"         
##  [7169] "Pp2d1"          "Aff3"           "Sgo1"           "Armcx3"        
##  [7173] "Pot1b"          "Stap2"          "Sh3gl1"         "Ubxn6"         
##  [7177] "Lrg1"           "Sema6b"         "Mydgf"          "Dpp9"          
##  [7181] "Chst10"         "Ticam1"         "Plin3"          "Arrdc5"        
##  [7185] "Ptprs"          "Znrf4"          "Safb2"          "Micos13"       
##  [7189] "Lonp1"          "Vmac"           "Nrtn"           "Tbc1d8"        
##  [7193] "Rfx2"           "Acsbg2"         "Mllt1"          "Pspn"          
##  [7197] "Gtf2f1"         "Khsrp"          "Slc25a23"       "C3"            
##  [7201] "Gpr108"         "Rpl7a-ps5"      "Xpo7"           "Rnf149"        
##  [7205] "Pdzph1"         "Nudt12"         "Fbxl17"         "AU016765"      
##  [7209] "Gm18736"        "Rab31"          "Twsg1"          "Ndufv2"        
##  [7213] "Mtcl1"          "Rab12"          "Gm5100"         "Ptprm"         
##  [7217] "Arhgap28"       "Tgif1"          "Myl12b"         "Myl12a"        
##  [7221] "Emilin2"        "Smchd1"         "Ndc80"          "Trmt61b"       
##  [7225] "Gm26963"        "Creg2"          "Xdh"            "Memo1"         
##  [7229] "Atp6v1f"        "Gm9351"         "Nlrc4"          "Fez2"          
##  [7233] "Strn"           "Heatr5b"        "Eif2ak2"        "Prkd3"         
##  [7237] "Mfsd9"          "Gm49869"        "Cdc42ep3"       "Cyp1b1"        
##  [7241] "Hnrnpll"        "Srsf7"          "Dhx57"          "Gm10190"       
##  [7245] "Sos1"           "Rpl31-ps25"     "Cox7a2l"        "Tgfbrap1"      
##  [7249] "Kcng3"          "Haao"           "Zfp36l2"        "Thada"         
##  [7253] "Prepl"          "Six3os1"        "Six2"           "Gm10309"       
##  [7257] "Stpg4"          "Calm2"          "Fhl2"           "Kcnk12"        
##  [7261] "Fbxo11"         "Lhcgr"          "Fshr"           "Mettl4"        
##  [7265] "Gm1976"         "Gm23102"        "Or10h28"        "Cul2"          
##  [7269] "Gm6235"         "Ccdc168"        "Lyzl1"          "Mtpap"         
##  [7273] "Rpl7a"          "Svil"           "BC025933"       "Zeb1"          
##  [7277] "Gm7464"         "4921524L21Rik"  "Rab18"          "Gm18948"       
##  [7281] "Tex30"          "Gm4833"         "Fzd8"           "Gm7527"        
##  [7285] "Gm5501"         "Thoc1"          "Greb1l"         "Snrpd1"        
##  [7289] "Gata6"          "Rbbp8"          "Rmc1"           "Poglut2"       
##  [7293] "Ttc39c"         "Gm50098"        "Rsl24d1"        "Dsg1b"         
##  [7297] "4930426D05Rik"  "Asxl3"          "Dtna"           "Mapre2"        
##  [7301] "Zfp397"         "Zfp35"          "Txn-ps1"        "Galnt1"        
##  [7305] "2700062C07Rik"  "Elp2"           "AW554918"       "Pik3c3"        
##  [7309] "B930094E09Rik"  "Sap130"         "Ammecr1l"       "Lims2"         
##  [7313] "Gm5969"         "Gm54825"        "Slc40a1"        "Ercc3"         
##  [7317] "Bin1"           "Wdr36"          "Camk4"          "Srp19"         
##  [7321] "Pkd2l2"         "Kif20a"         "n-R5s25"        "Kdm3b"         
##  [7325] "Reep2"          "Stk-ps2"        "Egr1"           "Ctnna1"        
##  [7329] "Snora74a"       "Pnet-ps"        "Paip2"          "Cxxc5"         
##  [7333] "4930471G03Rik"  "Pura"           "Cystm1"         "Eif4ebp3"      
##  [7337] "Slc39a10"       "Slc35a4"        "Ik"             "Wdr55"         
##  [7341] "Zmat2"          "Gm6756"         "Pcdhb3"         "Pcdhb8"        
##  [7345] "Pcdhb15"        "Dele1"          "Arhgap26"       "Gm28388"       
##  [7349] "Pabpc2"         "Kctd16"         "Cstdc7"         "Steep1"        
##  [7353] "Dcp2"           "Ythdc2"         "1700018A14Rik"  "Arl14epl"      
##  [7357] "Commd10"        "Hspe1"          "Myo1b"          "Gm5236"        
##  [7361] "Dmxl1"          "Tnfaip8"        "Fam170a"        "Prr16"         
##  [7365] "Srfbp1"         "Zfp474"         "Sncaip"         "Snx2"          
##  [7369] "Csnk1g3"        "Rpl15"          "Gm54362"        "Gramd2b"       
##  [7373] "Phax"           "Spmip10"        "Gm10536"        "Megf10"        
##  [7377] "Prrc1"          "Ccdc192"        "Slc27a6"        "Adamts19"      
##  [7381] "Gls"            "Minar2"         "2610318N02Rik"  "Rps14"         
##  [7385] "Cd74"           "Pdgfrb"         "Csf1r"          "Il17b"         
##  [7389] "Sh3tc2"         "Gm41750"        "Htr4"           "Nab1"          
##  [7393] "Apcdd1"         "Napg"           "St8sia3"        "Nedd4l"        
##  [7397] "Malt1"          "Sec11c"         "Pmaip1"         "Gnal"          
##  [7401] "Chmp1b"         "Impa2"          "Inpp1"          "Cidea"         
##  [7405] "Tubb6"          "Prelid3a"       "Psmg2"          "Seh1l"         
##  [7409] "Cep192"         "Ldlrad4"        "Rnmt"           "A730085E03Rik" 
##  [7413] "Tcf4"           "1700019D03Rik"  "Mbd2"           "Mex3c"         
##  [7417] "Mro"            "Cxxc1"          "Cfap53"         "Myo5b"         
##  [7421] "Acaa2"          "Dym"            "Gm10532"        "Smad2"         
##  [7425] "Dhrs1"          "1700019A02Rik"  "Skor2"          "Ier3ip1"       
##  [7429] "Hdhd2"          "St8sia5"        "Loxhd1"         "4930465K10Rik" 
##  [7433] "Pstpip2"        "Epg5"           "Pard6g"         "Slc66a2"       
##  [7437] "Stk17b"         "Gm17383"        "Zfp516"         "Ptgr3"         
##  [7441] "Gm2390"         "Cyb5a"          "Fbxo15"         "Rttn"          
##  [7445] "Tmx3"           "Gm45871"        "Zfp438"         "Hecw2"         
##  [7449] "Zeb1os1"        "Kif5b"          "Odad2"          "Mpp7"          
##  [7453] "Gm9993"         "Gm20147"        "Ccny"           "Cetn1"         
##  [7457] "Gm17430"        "Rock1"          "Gm34066"        "Esco1"         
##  [7461] "Abhd3"          "Tmem241"        "Npc1"           "Gm5240"        
##  [7465] "Zfp521"         "Kctd1"          "Cdh2"           "4921533I20Rik" 
##  [7469] "Rpl35"          "Pgap1"          "B4galt6"        "Garem1"        
##  [7473] "Klhl14"         "Ccdc178"        "Nol4"           "Zscan30"       
##  [7477] "Zfp24"          "Ino80c"         "Mir187"         "Rprd1a"        
##  [7481] "Ankrd44"        "Gm9955"         "Tpgs2"          "Gm5064"        
##  [7485] "Rps25"          "Bloc1s1"        "Gm41780"        "Gm7941"        
##  [7489] "Syt4"           "Myo7b"          "Proc"           "Hspd1"         
##  [7493] "Gypc"           "Stard4"         "Nrep"           "Epb41l4a"      
##  [7497] "Gm10548"        "Brd8dc"         "Brd8"           "Cdc23"         
##  [7501] "Gfra3"          "Cdc25c"         "Hsfy2"          "Etf1"          
##  [7505] "Sil1"           "Slc23a1"        "Prob1"          "Dnajc18"       
##  [7509] "Ecscr"          "Pfdn1"          "Hbegf"          "Sra1"          
##  [7513] "Apbb3"          "Satb2"          "E230025N22Rik"  "Ndufa2"        
##  [7517] "Hars1"          "Gm10545"        "Slc25a2"        "Taf7"          
##  [7521] "Uxt"            "Hdac3"          "Arap3"          "1700086O06Rik" 
##  [7525] "Tyw5"           "Pcdh12"         "Gnpda1"         "Spry4"         
##  [7529] "Fgf1"           "Plac8l1"        "Lars1"          "Gpr151"        
##  [7533] "Gm22264"        "Mcc"            "Gm4839"         "Vta1"          
##  [7537] "Clk1"           "Gm10540"        "Trim36"         "Pggt1b"        
##  [7541] "Ccdc112"        "Mospd4"         "Ticam2"         "Cdo1"          
##  [7545] "Atg12"          "Gm6883"         "Dtwd2"          "Ppil3"         
##  [7549] "Pudp"           "Ppic"           "Gm8594"         "Gm24514"       
##  [7553] "Gm26959"        "Aldh7a1"        "C330018D20Rik"  "Myoz3"         
##  [7557] "Synpo"          "Ndst1"          "Hycc2"          "Tcof1"         
##  [7561] "Slc6a7"         "Cdx1"           "Hmgxb3"         "Afap1l1"       
##  [7565] "Fech"           "Nars1"          "Atp8b1"         "Gm46618"       
##  [7569] "Lman1"          "Trak2"          "Ccbe1"          "Afg3l2"        
##  [7573] "Ptpn2"          "Fam210a"        "4930503L19Rik"  "Poli"          
##  [7577] "Rpl5"           "Gm54867"        "Smad4"          "Me2"           
##  [7581] "C2cd6"          "Ska1"           "Scarna17"       "Lipg"          
##  [7585] "Ctif"           "1700003O11Rik"  "Katnal2"        "Ark2c"         
##  [7589] "Ark2n"          "Haus1"          "Siglec15"       "Tmem237"       
##  [7593] "Setbp1"         "Adnp2"          "Rbfa"           "Kcng2"         
##  [7597] "Ctdp1"          "Atp9b"          "Sall3"          "Zfp236"        
##  [7601] "Gm54980"        "Timm21"         "Als2"           "Gm7612"        
##  [7605] "Gnpnat1"        "Gm5826"         "Socs6"          "Mrpl21"        
##  [7609] "Cpt1a"          "1810055G02Rik"  "Aldh3b3"        "Aldh3b2"       
##  [7613] "Acy3"           "Sumo1"          "Tbx10"          "Nudt8"         
##  [7617] "Cabp2"          "Cdk2ap2"        "Pitpnm1"        "Tmem134"       
##  [7621] "Coro1b"         "Ptprcap"        "Ppp1ca"         "Gm45928"       
##  [7625] "Ica1l"          "Pcx"            "Sptbn2"         "Rbm4b"         
##  [7629] "Ccdc87"         "Ctsf"           "Mrpl11"         "Slc29a2"       
##  [7633] "B4gat1"         "Brms1"          "Rin1"           "Wdr12"         
##  [7637] "Cd248"          "Yif1a"          "Gm10817"        "Eif1ad"        
##  [7641] "D330050I16Rik"  "AI837181"       "1810058N15Rik"  "Rela"          
##  [7645] "Map3k11"        "Kcnk7"          "Gm37035"        "Raph1"         
##  [7649] "Ltbp3"          "Slc25a45"       "Syvn1"          "Tmem262"       
##  [7653] "Cdca5"          "Lamtor1"        "Majin"          "Atg2a"         
##  [7657] "Mir194-2"       "Ehd1"           "Ino80d"         "Men1"          
##  [7661] "Map4k2"         "Pygm"           "Trmt112"        "Bad"           
##  [7665] "Ppp1r14b"       "Trpt1"          "Macrod1"        "Gm22113"       
##  [7669] "Rcor2"          "Ndufs1"         "Zfta"           "Iscu"          
##  [7673] "Slc22a8"        "Chrm1"          "Snord22"        "Wdr74"         
##  [7677] "Tmem223"        "Hnrnpul2"       "Ubxn1"          "Ints5"         
##  [7681] "Prelid1"        "Eml3"           "Mta2"           "Tut1"          
##  [7685] "Ahnak"          "Gm54995"        "Rab3il1"        "Fads3"         
##  [7689] "Gm10143"        "Syt7"           "Cyb561a3"       "4933402D24Rik" 
##  [7693] "Vwce"           "Vps37c"         "Slc15a3"        "Ms4a4b"        
##  [7697] "Mrpl16"         "Patl1"          "Gm17802"        "Mpeg1"         
##  [7701] "Rplp1rt"        "Or5b21"         "Klf7"           "Or10q1b"       
##  [7705] "Or10q12"        "Rpl37-ps1"      "Gna14"          "D030056L22Rik" 
##  [7709] "Trpm6"          "Aldh1a1"        "Zfand5"         "Abhd17b"       
##  [7713] "Trpm3"          "Fzd5"           "Nsa2"           "Mir204"        
##  [7717] "2410080I02Rik"  "Gm21542"        "Ptar1"          "Tmem252"       
##  [7721] "Cycs"           "Dock8"          "Gm5249"         "Dmrt1"         
##  [7725] "Akr1cl"         "Dmrt3"          "Smarca2"        "Vldlr"         
##  [7729] "Plpp6"          "Cdc37l1"        "Jak2"           "Cd274"         
##  [7733] "Mlana"          "Il33"           "Uhrf2"          "Crygc"         
##  [7737] "Cstf2t"         "A1cf"           "Sgms1os1"       "Minpp1"        
##  [7741] "Papss2"         "Pten"           "Nudt15"         "Lipf"          
##  [7745] "Stambpl1"       "Ifit3"          "Idh1"           "Kif20b"        
##  [7749] "Gm47773"        "Gm9042"         "Btaf1"          "Marchf5"       
##  [7753] "Kif11"          "Exoc6"          "Cyp26c1"        "Gm9067"        
##  [7757] "Cep55"          "Txndc12"        "Kansl1l"        "Gm23300"       
##  [7761] "Ffar4"          "Plce1"          "Tbc1d12"        "Hells"         
##  [7765] "Cyp2c55"        "Cyp2c66"        "Cyp2c29"        "Entpd1"        
##  [7769] "Cc2d2b"         "Acadl"          "Zfp518a"        "Dppa2"         
##  [7773] "Lcor"           "Frat1"          "Pgam1"          "Zdhhc16"       
##  [7777] "Ankrd2"         "4933411K16Rik"  "Pi4k2a"         "Marveld1"      
##  [7781] "Rpl31-ps14"     "Zfyve27"        "Golga7b"        "R3hcc1l"       
##  [7785] "Cnnm1"          "Nkx2-3"         "Cutc"           "Scd3"          
##  [7789] "Scd2"           "Hif1an"         "Pax2"           "Erbb4"         
##  [7793] "Gm5246"         "Slf2"           "Sema4g"         "Twnk"          
##  [7797] "Sfxn3"          "Tlx1"           "Dpcd"           "4930505N22Rik" 
##  [7801] "Pprc1"          "Nolc1"          "Gm8840"         "Nfkb2"         
##  [7805] "Fbxl15"         "Mir146b"        "Mfsd13a"        "Trim8"         
##  [7809] "Sfxn2"          "Taf5"           "Neurl1a"        "Slk"           
##  [7813] "Sfr1"           "Bard1"          "Gsto2"          "Cfap58"        
##  [7817] "Rpl31-ps18"     "Ins1"           "Add3"           "Smc3"          
##  [7821] "Rbm20"          "Shoc2"          "Acsl5"          "Vti1a"         
##  [7825] "Gm8870"         "Tcf7l2"         "Casp7"          "Nhlrc2"        
##  [7829] "Adrb1"          "Fhip2a"         "Gm50185"        "Ccdc172"       
##  [7833] "Gm9276"         "Slc18a2"        "Emx2"           "Fn1"           
##  [7837] "E330013P04Rik"  "Nanos1"         "Dennd10"        "Grk5"          
##  [7841] "Gm25431"        "Gm50307"        "Ppp6r3"         "Lrp5"          
##  [7845] "Tcirg1"         "Ndufs8"         "Gm5829"         "Aldh3b1"       
##  [7849] "Ndufv1"         "Gstp1"          "Aip"            "Rps6kb2"       
##  [7853] "Tbc1d10c"       "Rad9a"          "Ssh3"           "Rhod"          
##  [7857] "Lrfn4"          "Mreg"           "Rbm14"          "Dpp3"          
##  [7861] "Peli3"          "Npas4"          "Tmem151a"       "Rab1b"         
##  [7865] "Klc2"           "Pacs1"          "Sf3b2"          "Banf1"         
##  [7869] "Aup1"           "Marchf4"        "Sart1"          "Tsga10ip"      
##  [7873] "Gm6293"         "Ccdc85b"        "Mus81"          "Snx32"         
##  [7877] "Nscme3l"        "Kat5"           "Pcnx3"          "Ehbp1l1"       
##  [7881] "Igfbp5"         "Malat1"         "Frmd8"          "Tigd3"         
##  [7885] "Cdc42ep2"       "Pola2"          "Tm7sf2"         "Zfpl1"         
##  [7889] "Snx15"          "Arl2"           "Slc22a12"       "Tnp1"          
##  [7893] "Gm14964"        "Rps6ka4"        "Ccdc88b"        "Catsperz"      
##  [7897] "Kcnk4"          "Plcb3"          "Fkbp2"          "Dnajc4"        
##  [7901] "Nudt22"         "Fermt3"         "Tns1"           "Stip1"         
##  [7905] "Otub1"          "Cox8a"          "Mark2"          "Spindoc"       
##  [7909] "Slc3a2"         "Tmem179b"       "Taf6l"          "Polr2g"        
##  [7913] "Ttc9c"          "Aamp"           "Gng3"           "Uqcc3"         
##  [7917] "5730408K05Rik"  "Rom1"           "Incenp"         "Best1"         
##  [7921] "Gm50359"        "Fen1"           "Myrf"           "Lrrc10b"       
##  [7925] "Tmbim1"         "Sdhaf2"         "Tmem138"        "Cd5"           
##  [7929] "Tmem132a"       "Tmem109"        "Zp1"            "Ccdc86"        
##  [7933] "Ms4a15"         "Ms4a20"         "Ms4a19"         "Zfp142"        
##  [7937] "Ms4a13"         "Ms4a5"          "Ms4a14"         "Or10q3"        
##  [7941] "Gm6365"         "Or5bb10"        "Or5an1c"        "Or5a21"        
##  [7945] "Dtx4"           "Or5b125-ps1"    "Rnf25"          "Or9q2"         
##  [7949] "Tle4"           "Psat1"          "Foxb2"          "Ostf1"         
##  [7953] "Gm22684"        "Anxa1"          "Aldh1a7"        "Tmc1"          
##  [7957] "Gda"            "Prkag3"         "Cfap95"         "Entrep1"       
##  [7961] "Fxn"            "Pabir1"         "Zng1"           "Gm34432"       
##  [7965] "Pum3"           "Rfx3"           "Glis3"          "Insl6"         
##  [7969] "Fev"            "Ermp1"          "Brd10"          "Ranbp6"        
##  [7973] "Ppp1r2-ps3"     "Dkk1"           "Prkg1"          "Asah2"         
##  [7977] "Rnls"           "Lipo3"          "Ankrd22"        "Zranb1"        
##  [7981] "Cryba2"         "Acta2"          "Lipa"           "Pank1"         
##  [7985] "Mir107"         "Ankrd1"         "F530104D19Rik"  "Fgfbp3"        
##  [7989] "Cpeb3"          "Myof"           "Rbp4"           "Cfap65"        
##  [7993] "Fra10ac1"       "Ctdspl2"        "Pdlim1"         "Sorbs1"        
##  [7997] "Aldh18a1"       "Tctn3"          "Pik3ap1"        "Rrp12"         
##  [8001] "Exosc1"         "Mms19"          "Ihh"            "Morn4"         
##  [8005] "Avpi1"          "Crtac1"         "Loxl4"          "Pyroxd2"       
##  [8009] "Got1"           "Dnmbp"          "Cpn1"           "Cyp2c23"       
##  [8013] "Erlin1"         "Cnppd1"         "Chuk"           "Cwf19l1"       
##  [8017] "Bloc1s2"        "Pkd2l1"         "Scd1"           "Ndufb8"        
##  [8021] "Pdzd7"          "Lbx1"           "Poll"           "Fbxw4"         
##  [8025] "Abcb6"          "Fgf8"           "Oga"            "Kcnip2"        
##  [8029] "Armh3"          "Pitx3"          "Psd"            "Cuedc2"        
##  [8033] "2310034G01Rik"  "Actr1a"         "Arl3"           "Atg9a"         
##  [8037] "Cyp17a1"        "Pcgf6"          "Calhm3"         "Sh3pxd2a"      
##  [8041] "Stn1"           "Col17a1"        "Cfap43"         "Itprip"        
##  [8045] "1700001K23Rik"  "Smndc1"         "Tuba4a"         "Mirt1"         
##  [8049] "Gucy2g"         "Zdhhc6"         "Dclre1a"        "Ccdc186"       
##  [8053] "Ablim1"         "Gfra1"          "Hspa12a"        "Shtn1"         
##  [8057] "Vax1"           "Dnpep"          "Pdzd8"          "Fam204a"       
##  [8061] "Eif3a"          "Sfxn4"          "Prdx3"          "Zfp950"        
##  [8065] "Mplkipl1"       "Csf2ra"         "Lax1"           "Fam171a1"      
##  [8069] "Obsl1"          "Dclre1c"        "Phxr1"          "Cdnf"          
##  [8073] "Fam107b"        "Frmd4a"         "Gm10862"        "Bend7"         
##  [8077] "Sephs1"         "Phyh"           "Ccdc3"          "Pax3"          
##  [8081] "Nudt5"          "Usp6nl"         "Gata3os"        "C630004M23Rik" 
##  [8085] "Kin"            "Itih5"          "Mir669b"        "Mir297b"       
##  [8089] "Gm10851"        "Il2ra"          "Ube2g1"         "BC031181"      
##  [8093] "Farsb"          "Il15ra"         "Ankrd16"        "Stam"          
##  [8097] "Mrc1"           "Cacnb2"         "Arl5b"          "Gm13365"       
##  [8101] "Plxdc2"         "Gm25147"        "Spag6"          "BC035947"      
##  [8105] "4930426L09Rik"  "Msrb2"          "1810010K12Rik"  "Otud1"         
##  [8109] "Etl4"           "Gad2"           "1700092C17Rik"  "Apbb1ip"       
##  [8113] "Pdss1"          "Acbd5"          "Wdfy1"          "Yme1l1"        
##  [8117] "Ankrd68"        "Gm13410"        "Il1rn"          "Dph7"          
##  [8121] "Nsmf"           "Tmem203"        "Tprn"           "Tmem210"       
##  [8125] "Lrrc26"         "Serpine2"       "Man1b1"         "Sapcd2"        
##  [8129] "Entpd2"         "Npdc1"          "Abca2"          "Clic3"         
##  [8133] "Edf1"           "Fcnaos"         "Bmyc"           "Dipk1b"        
##  [8137] "Slc25a5"        "Surf2"          "Stkld1"         "Cacfd1"        
##  [8141] "Gm13397"        "Adamtsl2"       "Rxra"           "Ppp1r26"       
##  [8145] "Gbgt1"          "Gm10134"        "Ralgds"         "Fam124b"       
##  [8149] "Ddx31"          "Ttf1"           "Med27"          "Rapgef1"       
##  [8153] "Gm13547"        "Coq4"           "Slc27a4"        "Cercam"        
##  [8157] "Tbc1d13"        "Endog"          "Gm17764"        "Lrrc8a"        
##  [8161] "Phyhd1"         "Dolpp1"         "Ptpa"           "Ntmt1"         
##  [8165] "Tor1b"          "Gpr107"         "Ncs1"           "Hmcn2"         
##  [8169] "Fubp3"          "Sphkap"         "Exosc2"         "Abl1"          
##  [8173] "Aif1l"          "Plpp7"          "Pomt1"          "Golga2"        
##  [8177] "Ciz1"           "Naif1"          "Eeig1"          "Pip5kl1"       
##  [8181] "Slc16a14"       "St6galnac6"     "Ak1"            "Eng"           
##  [8185] "Tor2a"          "Gm24165"        "Niban2"         "Angptl2"       
##  [8189] "Cntrl"          "Gsn"            "Glo1"           "Ncl"           
##  [8193] "Morn5"          "Mrrf"           "Or1n2"          "Lhx2"          
##  [8197] "Gm25081"        "Gm13588"        "Olfml2a"        "Wdr38"         
##  [8201] "Gm13456"        "Acvr2a"         "Tmem165"        "Alppl2"        
##  [8205] "Mbd5"           "Epc2"           "Kif5c"          "Lypd6b"        
##  [8209] "Gm13498"        "Rif1"           "Arl6ip6"        "Gm25489"       
##  [8213] "Gpd2"           "Pkp4"           "Ngef"           "Dapl1"         
##  [8217] "Ldha-ps"        "Tank"           "Psmd14"         "Gca"           
##  [8221] "Scn2a"          "Csrnp3"         "Tax1bp3"        "4933409G03Rik" 
##  [8225] "Cers6"          "Usp40"          "Ppig"           "Ssb"           
##  [8229] "Ubr3"           "Myo3b"          "Sp5"            "Gad1"          
##  [8233] "Dcaf17"         "Hat1"           "Metap1d"        "Platr26"       
##  [8237] "Dnajb3"         "Itga6"          "Pdk1"           "Rapgef4"       
##  [8241] "Map3k20"        "Cdca7"          "Ak4"            "Sp3os"         
##  [8245] "Sp9"            "Scrn3"          "Hoxd13"         "Glrp1"         
##  [8249] "Hoxd10"         "Hoxd8"          "Hoxd4"          "Hoxd1"         
##  [8253] "Mtx2"           "Agps"           "Rbm45"          "Ube2e3"        
##  [8257] "Itprid2"        "Prdx6b"         "Arl4c"          "Dnajc10"       
##  [8261] "Gm13687"        "Dusp19"         "Nup35"          "Gm13675"       
##  [8265] "Fsip2"          "Itgav"          "Med19"          "Ypel4"         
##  [8269] "Timm10"         "Gbx2"           "Ssrp1"          "Tnks1bp1"      
##  [8273] "Gm13735"        "Or12e8"         "Mtch2"          "C1qtnf4"       
##  [8277] "Kbtbd4"         "Celf1"          "Rapsn"          "Psmc3"         
##  [8281] "Iqca1"          "Mybpc3"         "Acp2"           "Pacsin3"       
##  [8285] "Arhgap1"        "Harbi1"         "Ambra1"         "Gm9821"        
##  [8289] "Phf21a"         "Pex16"          "Frey1"          "Col6a3"        
##  [8293] "Chst1"          "Syt13"          "Alkbh3os1"      "2810002D19Rik" 
##  [8297] "Commd9"         "Pamr1"          "Slc1a2"         "Apip"          
##  [8301] "Lmo2"           "Cd59b"          "Rab17"          "Cd59a"         
##  [8305] "A930018P22Rik"  "Gm13882"        "Ccdc73"         "Wt1"           
##  [8309] "Immp1l"         "Gm9342"         "Kif18a"         "Bdnf"          
##  [8313] "Lin7c"          "Mrpl43"         "Ilkap"          "Lgr4"          
##  [8317] "Ccdc34"         "Gm13961"        "Or4k36"         "Or4g7"         
##  [8321] "Lpcat4"         "Nop10"          "Gm21985"        "Katnbl1"       
##  [8325] "Aven"           "Hes6"           "Tmco5b"         "Cdin1"         
##  [8329] "Tmco5"          "Spred1"         "Mir674"         "Gm25189"       
##  [8333] "Fam98b"         "Bub1b"          "Inafm2"         "Knstrn"        
##  [8337] "Per2"           "Bahd1"          "Rad51"          "Gm14137"       
##  [8341] "Zfyve19"        "Spint1"         "Vps18"          "Chac1"         
##  [8345] "Chp1"           "Nusap1"         "Itpka"          "Hdac4"         
##  [8349] "Mga"            "Mapkbp1"        "Snap23"         "Haus2"         
##  [8353] "Stard9"         "AV039307"       "Tmem62"         "Ccndbp1"       
##  [8357] "Adal"           "Map1a"          "Ndufa10"        "Ckmt1"         
##  [8361] "Hypk"           "Wdr76"          "Golm2"          "B2m"           
##  [8365] "Terb2"          "Afg2b"          "AA467197"       "Bloc1s6"       
##  [8369] "Sqor"           "Cops9"          "Sema6d"         "Dut"           
##  [8373] "Eid1"           "Dtwd1"          "Ap4e1"          "Stard7"        
##  [8377] "Adra2b"         "Mrps5"          "Acoxl"          "Spdye4c"       
##  [8381] "Otos"           "Mertk"          "Fbln7"          "Zc3h6"         
##  [8385] "Polr1b"         "Chchd5"         "Il1bos"         "Sirpa"         
##  [8389] "Stk35"          "Tgm3"           "Nop56"          "Ankmy1"        
##  [8393] "Snord57"        "Ebf4"           "1700020A23Rik"  "Tmem239"       
##  [8397] "Vps16"          "Ptpra"          "Mrps26"         "Oxt"           
##  [8401] "Itpa"           "Atrn"           "9430060I03Rik"  "Ap5s1"         
##  [8405] "Pank2"          "Mir103-2"       "Smox"           "Prnp"          
##  [8409] "Prn"            "Cds2"           "Chgb"           "Mcm8"          
##  [8413] "Plcb1"          "Kif1a"          "Plcb4"          "Ankef1"        
##  [8417] "Slx4ip"         "Btbd3"          "Macrod2"        "Snrpb2"        
##  [8421] "Dstn"           "Banf2"          "Mgme1"          "Kat14"         
##  [8425] "Mrpl52"         "Mab21l4"        "Zfp133-ps"      "Polr3f"        
##  [8429] "Sec23b"         "Dtd1"           "Scp2d1"         "Slc24a3"       
##  [8433] "Naa20"          "Cfap61"         "Insm1"          "Xrn2"          
##  [8437] "Pask"           "6430503K07Rik"  "Gm14113"        "Gm14106"       
##  [8441] "A530006G24Rik"  "Nxt1"           "Cstl1"          "Cstdc1"        
##  [8445] "Cst12"          "Cst8"           "Cst13"          "Thap4"         
##  [8449] "Cst9"           "Fndc10l"        "Syndig1"        "Entpd6"        
##  [8453] "Pygb"           "Gins1"          "Gm14149"        "Gm14148"       
##  [8457] "Nsfl1c"         "Fkbp1a"         "Pdcd1"          "Sdcbp2"        
##  [8461] "Angpt4"         "Scrt2"          "Tcf15"          "Csnk2a1"       
##  [8465] "Gm14165"        "6820408C15Rik"  "Defb20"         "Defb21"        
##  [8469] "Defb36"         "Gm5264"         "Mcts2"          "Gm14162"       
##  [8473] "Cox4i2"         "Tpx2"           "Ttll9"          "Xkr7"          
##  [8477] "Ccm2l"          "Hck"            "Tm9sf4"         "Kif3b"         
##  [8481] "Slco6b1"        "Asxl1"          "Dnmt3b"         "Tomm20"        
##  [8485] "Bpifb2"         "Bpifb3"         "Bpifa3"         "Bpifb5"        
##  [8489] "Cbfa2t2"        "1700003F12Rik"  "Actl10"         "Slco6c1"       
##  [8493] "Zfp341"         "Chmp4b"         "Raly"           "a"             
##  [8497] "Dynlrb1"        "Map1lc3a"       "Trp53inp2"      "Acss2"         
##  [8501] "Myh7b"          "Procr"          "Macir"          "Cep250"        
##  [8505] "Spag4"          "Romo1"          "Cnbd2"          "Epb41l1"       
##  [8509] "Aar2"           "Dlgap4"         "Myl9"           "Tgif2"         
##  [8513] "Rab5if"         "Pam"            "Src"            "Nnat"          
##  [8517] "Ctnnbl1"        "Vstm2l"         "Rprd1b"         "Bpi"           
##  [8521] "Lbp"            "Adig"           "Arhgap40"       "Slc32a1"       
##  [8525] "Pign"           "Ppp1r16b"       "Fam83d"         "4933416E03Rik" 
##  [8529] "Top1"           "Plcg1"          "Lpin3"          "Gm14243"       
##  [8533] "Gm11452"        "L3mbtl1"        "Sgk2"           "Cdv3"          
##  [8537] "Bcl2"           "Ift52"          "Mybl2"          "Tox2"          
##  [8541] "Gdap1l1"        "Hnf4a"          "Ttpal"          "Pkig"          
##  [8545] "Ccn5"           "Kcnk15"         "Ywhab"          "Kdsr"          
##  [8549] "Pabpc1l"        "Svs5"           "Dbndd2"         "Pigt"          
##  [8553] "Dnttip1"        "Ube2c"          "Snx21"          "Zswim3"        
##  [8557] "Zswim1"         "Ctsa"           "Vps4b"          "Pcif1"         
##  [8561] "Cd40"           "Ncoa3"          "Trp53rkb"       "Arfgef2"       
##  [8565] "Ddx27"          "Zfas1"          "Slc9a8"         "Cebpb"         
##  [8569] "A530013C23Rik"  "Tsn"            "Ptpn1"          "Mocs3"         
##  [8573] "Tshz2"          "Hax1"           "Pfdn4"          "Fam210b"       
##  [8577] "Cstf1"          "Rtf2"           "Tfap2c"         "Spo11"         
##  [8581] "Inhbb"          "Rbm38"          "Pck1"           "Cimip1"        
##  [8585] "Rab22a"         "1700010B08Rik"  "Stx16"          "Nelfcd"        
##  [8589] "Tubb1"          "Gm14439"        "Gm14296"        "Tmem177"       
##  [8593] "Gm14403"        "Zfp971"         "Fam217b"        "Cdh26"         
##  [8597] "Wtap"           "4930591A17Rik"  "Cdh4"           "Lsm14b"        
##  [8601] "Ss18l1"         "Osbpl2"         "Cfap221"        "Adrm1"         
##  [8605] "Rps21"          "Gata5os"        "Mrgbp"          "Ogfr"          
##  [8609] "Col9a3"         "Gid8"           "Slc17a9"        "Arfgap1"       
##  [8613] "Ppdpf"          "Tmem37"         "Fndc11"         "Rtel1"         
##  [8617] "Zgpat"          "Slc2a4rg-ps"    "Abhd16b"        "Tpd52l2"       
##  [8621] "Dnajc5"         "Prpf6"          "Tcea2"          "Oprl1"         
##  [8625] "Dbi"            "Myt1"           "Pcmtd2"         "Polr3k"        
##  [8629] "Gm5466"         "Rpp38"          "Suv39h2"        "Prpf18"        
##  [8633] "Optn"           "Camk1d"         "Sec61a2"        "Marco"         
##  [8637] "Proser2"        "Gm13384"        "Echdc3"         "Gm10855"       
##  [8641] "Slc25a36"       "Gata3"          "Taf3"           "Atp5f1c"       
##  [8645] "Itih2"          "Pfkfb3"         "Ncstn"          "Insig2"        
##  [8649] "Rbm17"          "Fbh1"           "Gm13310"        "Itga8"         
##  [8653] "Mindy3"         "C1ql3"          "Rsu1"           "St8sia6"       
##  [8657] "Nsun6"          "H2al2a"         "Htr5b"          "Dnajc1"        
##  [8661] "Pip4k2a"        "4921504E06Rik"  "Arhgap21"       "Gm13377"       
##  [8665] "Enkur"          "Abi1"           "Mastl"          "Spopl"         
##  [8669] "Pax8"           "Ddx18"          "Gm13416"        "Cacna1b"       
##  [8673] "Noxa1"          "Tor4a"          "Nelfb"          "Stpg3"         
##  [8677] "Slc34a3"        "Ssna1"          "Uap1l1"         "Paxx"          
##  [8681] "Nckap5"         "Ptgds"          "Lcn12"          "Traf2"         
##  [8685] "Phpt1"          "Ajm1"           "Rabl6"          "Ccdc183"       
##  [8689] "Fcna"           "Sohlh1"         "Camsap1"        "Rpl27a"        
##  [8693] "Ubac1"          "Nacc2"          "Qsox2"          "Ccdc187"       
##  [8697] "Card9"          "Snapc4"         "Notch1"         "Gm13359"       
##  [8701] "Surf6"          "Med22"          "Tmem163"        "Surf1"         
##  [8705] "Rexo4"          "Mymk"           "Fam163b"        "Sardh"         
##  [8709] "Vav2"           "Brd3"           "Gm13372"        "Pierce1"       
##  [8713] "Gtf3c5"         "Zranb3"         "Gfi1b"          "Spaca9"        
##  [8717] "Gtf3c4"         "Barhl1"         "Cfap77"         "Trub2"         
##  [8721] "2600006K01Rik"  "Dync2i2"        "Zdhhc12"        "Spout1"        
##  [8725] "Mcm6"           "Kyat1"          "1700084E18Rik"  "Dolk"          
##  [8729] "1700001O22Rik"  "Asb6"           "BC005624"       "Fnbp1"         
##  [8733] "Qrfp"           "Fibcd1"         "Swi5"           "Cxcr4"         
##  [8737] "Dnm1"           "Bbln"           "Lcn2"           "Slc25a25"      
##  [8741] "9430097D07Rik"  "Cdk9"           "Ttc16"          "Cfap157"       
##  [8745] "Stxbp1"         "Lrsam1"         "Cd55b"          "Slc2a8"        
##  [8749] "Garnl3"         "Zbtb43"         "Lmx1b"          "Pbx3"          
##  [8753] "Gapvd1"         "Rabepk"         "Fbxw2"          "Psmd5"         
##  [8757] "Phf19"          "Ctbp1"          "Cd55"           "Traf1"         
##  [8761] "4930568D16Rik"  "Rbm18"          "Gm13436"        "Or12k8"        
##  [8765] "Or1b1"          "Pdcl"           "Zbtb6"          "Zbtb26"        
##  [8769] "Strbp"          "Il24"           "Psmb7"          "Nr5a1"         
##  [8773] "Golga1"         "Ppp6c"          "Gm13458"        "Zeb2"          
##  [8777] "Orc4"           "Mmadhc"         "Gm13487"        "Rnd3"          
##  [8781] "Mapkapk2"       "Rbm43"          "Arl5a"          "Cacnb4"        
##  [8785] "Stam2"          "Prpf40a"        "Gm13501"        "Rprm"          
##  [8789] "Gm13531"        "Cytip"          "Acvr1"          "Rassf5"        
##  [8793] "Ccdc148"        "Baz2b"          "Gm13570"        "Cd302"         
##  [8797] "Rbms1"          "Gm13576"        "Grb14"          "Cobll1"        
##  [8801] "Ttc21b"         "Scn7a"          "Ikbke"          "Spc25"         
##  [8805] "Abcb11"         "Cfap210"        "Mettl5"         "Gm26558"       
##  [8809] "Tlk1"           "Mettl8"         "Slc25a12"       "Dlx2"          
##  [8813] "Eif1-ps3"       "Mfsd4a"         "Ola1"           "Chn1"          
##  [8817] "Atp5mc3"        "Gm13668"        "Lnpk"           "Mrpl23"        
##  [8821] "Evx2"           "Hoxd3os1"       "Haglr"          "Nfe2l2"        
##  [8825] "Tmcc2"          "Ift70b"         "Ift70a1"        "Prkra"         
##  [8829] "Fkbp7"          "Ttn"            "Sestd1"         "Zfp385b"       
##  [8833] "Cwc22"          "Cerkl"          "Pde1a"          "Cntn2"         
##  [8837] "Frzb"           "Rps4x"          "Zswim2"         "Calcrl"        
##  [8841] "Tfpi"           "Selenoh"        "Clp1"           "Serping1"      
##  [8845] "Smtnl1"         "Rtn4rl2"        "Gm26616"        "P2rx3"         
##  [8849] "Lrrc55"         "Gm13719"        "Or5d16"         "Or5d44"        
##  [8853] "Or4c119"        "Or4c121"        "Or4c58"         "Or4b13"        
##  [8857] "Or4b1b"         "Sox13"          "Ptprj"          "Ndufs3"        
##  [8861] "Ptpmt1"         "Slc39a13"       "Madd"           "Nr1h3"         
##  [8865] "Ddb2"           "Zfp408"         "Atg13"          "Dgkz"          
##  [8869] "Abhd16a"        "Snrpe"          "Creb3l1"        "Large2"        
##  [8873] "Mapk8ip1"       "Cry2"           "Prdm11"         "Tspan18"       
##  [8877] "Cd82"           "Ext2"           "Gm13889"        "Hsd17b12"      
##  [8881] "Atp2b4"         "Mir670hg"       "Ttc17"          "Api5"          
##  [8885] "Iftap"          "Fjx1"           "Pdhx"           "Ehf"           
##  [8889] "Cat"            "4931422A03Rik"  "D430041D05Rik"  "Prelp"         
##  [8893] "Tcp11l1"        "Eif3m"          "Wt1os"          "Rcn1"          
##  [8897] "Elp4"           "Arl14ep"        "Mettl15"        "Gm13937"       
##  [8901] "Bbox1"          "Or4k35"         "Btg2"           "Nutm1"         
##  [8905] "Ryr3"           "Scg5"           "Arhgap11a"      "Actc1"         
##  [8909] "Zfp770"         "Dph6"           "Rab5b"          "Fsip1"         
##  [8913] "Srp14"          "Ppfia4"         "Bmf"            "Plcb2"         
##  [8917] "Ccdc9b"         "Rmdn3"          "Dnajc17"        "Ino80"         
##  [8921] "Exd1"           "Oip5"           "Ltk"            "Ndufaf1"       
##  [8925] "Mgat4e"         "Rpap1"          "Gm13998"        "Gm13999"       
##  [8929] "Ehd4"           "Pla2g4d"        "Tmem87a"        "Zfp106"        
##  [8933] "Lrrc57"         "Cdan1"          "Ttbk2"          "Ppp1r12b"      
##  [8937] "Ubr1"           "Lcmt2"          "Zscan29"        "Ell3"          
##  [8941] "Mageb3"         "Patl2"          "Shf"            "Slc30a4"       
##  [8945] "Myef2"          "Fbn1"           "Ptprv"          "Cep152"        
##  [8949] "Secisbp2l"      "Cops2"          "Fam227b"        "Hdc"           
##  [8953] "Trpm7"          "Sppl2a"         "Ncaph"          "1810024B03Rik" 
##  [8957] "Gm10766"        "Gpr37l1"        "Kcnip3"         "Zfp661"        
##  [8961] "Mal"            "Mall"           "Mtln"           "Bub1"          
##  [8965] "Morrbid"        "Gm14006"        "Ckap2l"         "Gm25703"       
##  [8969] "Rnpep"          "Cpxm1"          "4930473A02Rik"  "Avp"           
##  [8973] "Lzts3"          "Ddrgk1"         "Gfra4"          "Adam33"        
##  [8977] "Siglec1"        "Spef1"          "Cenpb"          "Sar1a"         
##  [8981] "Timm17a"        "Rnf24"          "Adra1d"         "Rassf2"        
##  [8985] "Tmem230"        "Pcna"           "Lrrn4"          "Tmx4"          
##  [8989] "Gm14053"        "Jag1"           "Rps19-ps7"      "Nav1"          
##  [8993] "Esf1"           "Sel1l2"         "Gm23846"        "Bfsp1"         
##  [8997] "Rrbp1"          "Gm5535"         "Snx5"           "Ovol2"         
##  [9001] "Dzank1"         "Rbbp9"          "Pkp1"           "Crnkl1"        
##  [9005] "Nkx2-4"         "Nkx2-2"         "Gm14115"        "Thbd"          
##  [9009] "Cd93"           "Cstdc2"         "Cst3"           "Gm10750"       
##  [9013] "C530025M09Rik"  "Mroh3"          "Zfp1001"        "3300002I08Rik" 
##  [9017] "Gm14122"        "Zfp442"         "Apmap"          "Acss1"         
##  [9021] "Abhd12"         "Ninl"           "4921509C19Rik"  "Snph"          
##  [9025] "Inava"          "Psmf1"          "Fam110a"        "Rbck1"         
##  [9029] "Trib3"          "Sox12"          "Defb29"         "Defb19"        
##  [9033] "Defb45"         "Defb25"         "Foxs1"          "Nek7"          
##  [9037] "Dusp15"         "Pdrg1"          "Plagl2"         "Nol4l"         
##  [9041] "Commd7"         "Sun5"           "Cdk5rap1"       "Necab3"        
##  [9045] "Pxmp4"          "4930519P11Rik"  "Cfhr1"          "Eif2s2"        
##  [9049] "Ncoa6"          "Gm14239"        "Gss"            "Edem2"         
##  [9053] "Eif6"           "Fam83c"         "Uqcc1"          "Gdf5"          
##  [9057] "6430550D23Rik"  "Cfhr3"          "Nfs1"           "Scand1"        
##  [9061] "Pdcd10"         "Norad"          "5730471H19Rik"  "4930518I15Rik" 
##  [9065] "Sla2"           "Dsn1"           "Mtcl2"          "Samhd1"        
##  [9069] "Cfh"            "Ghrh"           "Blcap"          "Tti1"          
##  [9073] "Tgm2"           "D630003M21Rik"  "Gm826"          "Mafb"          
##  [9077] "Chd6"           "Ptprt"          "Gm56286"        "Gm4845"        
##  [9081] "Gm11453"        "Gtsf1l"         "Jph2"           "Fitm2"         
##  [9085] "Hnf4aos"        "Ada"            "Rims4"          "Tomm34"        
##  [9089] "Wfdc5"          "Wfdc15a"        "Gm12902"        "Ro60"          
##  [9093] "Matn4"          "Trp53tg5"       "Wfdc6a"         "Eppin"         
##  [9097] "Wfdc11"         "Wfdc3"          "Tnnc2"          "Spata25"       
##  [9101] "Pltp"           "4930445K14Rik"  "Rgs2"           "Zfp335"        
##  [9105] "Cdh22"          "Slc35c2"        "Elmo2"          "Zfp334"        
##  [9109] "Ocstamp"        "Slc13a3"        "Trp53rka"       "Zmynd8"        
##  [9113] "Sulf2"          "Pla2g4a"        "Znfx1"          "Gm11472"       
##  [9117] "Kcnb1"          "Ptgis"          "B4galt5"        "Spata2"        
##  [9121] "Peds1"          "Ripor3"         "Kcng1"          "Atp9a"         
##  [9125] "Bex4"           "Sall4"          "Zfp64"          "Zfp217"        
##  [9129] "Bcas1"          "Cbln4"          "Aurka"          "Bmp7"          
##  [9133] "Zbp1"           "Pmepa1"         "Ppp4r1l-ps"     "Odr4"          
##  [9137] "Mir296"         "Ctsz"           "Atp5f1e"        "Prelid3b"      
##  [9141] "Gm14407"        "Ppp1r3d"        "Taf4"           "Psma7"         
##  [9145] "Cables2"        "Gata5"          "Hmcn1"          "Gm14340"       
##  [9149] "Nkain4"         "Eef1a2"         "Gmeb2"          "Arfrp1"        
##  [9153] "Zfp512b"        "Sox18"          "Rgs19"          "Gm2077"        
##  [9157] "Zc2hc1a"        "Gm10138"        "Gm7103"         "Gm5841"        
##  [9161] "Myef2l"         "Lrrcc1"         "E2f5"           "Car2"          
##  [9165] "Cypt12"         "Gm7442"         "Cp"             "Hltf"          
##  [9169] "Swt1"           "Tbl1xr1"        "Rprl2"          "Spin3-ps"      
##  [9173] "Spata16"        "Tnfsf10"        "Ghsr"           "Pld1"          
##  [9177] "Tnik"           "Slc2a2"         "Gm1527"         "Rnf2"          
##  [9181] "Mir551b"        "Mynn"           "Lrriq4"         "Sec62"         
##  [9185] "Gpr160"         "Skil"           "Cldn11"         "Kcnmb2"        
##  [9189] "Zfp639"         "Actl6a"         "Cox7b"          "Ndufb5"        
##  [9193] "Ttc14"          "Gm5708"         "Sox2"           "Gm7741"        
##  [9197] "Acad9"          "Exosc9"         "Bltp1"          "Gm12582"       
##  [9201] "Fgf2"           "Golga7"         "Mir6942"        "1700025G04Rik" 
##  [9205] "Afg2a"          "Rps23"          "Fat4"           "Intu"          
##  [9209] "Plk4"           "Gm22043"        "Larp1b"         "D3Ertd751e"    
##  [9213] "Pcdh10"         "Gm20557"        "Tsen15"         "4930577N17Rik" 
##  [9217] "Mgst2"          "Gm10729"        "Foxo1"          "Lhfpl6"        
##  [9221] "Proser1"        "Postn"          "Alg5"           "Smad9"         
##  [9225] "Spart"          "Rgl1"           "Ccdc169"        "Sohlh2"        
##  [9229] "Tm4sf4"         "Eif2a"          "Selenot"        "Gm9696"        
##  [9233] "Mbnl1"          "Rap2b"          "Mme"            "Kcnab1"        
##  [9237] "Gm7278"         "Gm54743"        "Acsf2"          "Tiparp"        
##  [9241] "Gm5847"         "Lekr1"          "Gm6555"         "Rsrc1"         
##  [9245] "Mfsd1"          "Smc4"           "Mir15b"         "Lamc1"         
##  [9249] "Ppm1l"          "Nmd3"           "Gm8604"         "Serpini1"      
##  [9253] "Spmip2"         "4930589L23Rik"  "Ppid"           "4930579G24Rik" 
##  [9257] "Ctso"           "Asic5"          "Npl"            "Sfrp2"         
##  [9261] "Gm7115"         "Gatb"           "Higd1a"         "Gm25188"       
##  [9265] "Lrba"           "Gm25039"        "Cd1d2"          "Etv3"          
##  [9269] "Etv3l"          "Rgsl1"          "Hdgf"           "Gpatch4"       
##  [9273] "Mef2d"          "Glmp"           "Smg5"           "Paqr6"         
##  [9277] "Ubqln4"         "Ssr2"           "Gon4l"          "Gm23054"       
##  [9281] "Teddm2"         "Pklr"           "Gm45927"        "Entrep3"       
##  [9285] "Gba1"           "Thbs3"          "Muc1"           "Krtcap2"       
##  [9289] "Dpm3"           "Dcst2"          "Shc1"           "Ier5"          
##  [9293] "Pygo2"          "Pmvk"           "Ube2q1"         "4933434E20Rik" 
##  [9297] "Tpm3"           "Nup210l"        "Rab13"          "Jtb"           
##  [9301] "Slc39a1"        "Crtc2"          "Mr1"            "Gatad2b"       
##  [9305] "S100a13"        "S100a7a"        "Pglyrp3"        "Sprr2a3"       
##  [9309] "Sprr2d"         "Gm18432"        "Flg"            "Tchh"          
##  [9313] "Tdpoz3"         "Gm20695"        "Gm5532"         "Spopfm2"       
##  [9317] "Them4"          "Rorc"           "Lingo4"         "Tdrkh"         
##  [9321] "Celf3"          "Selenbp2"       "Selenbp1"       "Vps72"         
##  [9325] "Tmod4"          "Lhx4"           "Cers2"          "Arnt"          
##  [9329] "Ctss"           "Golph3l"        "Ensa"           "Mcl1"          
##  [9333] "H2bc21"         "Gm24136"        "Hjv"            "Txnip"         
##  [9337] "Cep350"         "Ankrd34a"       "Lix1l"          "Rbm8a"         
##  [9341] "Pex11b"         "Itga10"         "Ankrd35"        "Rnf115"        
##  [9345] "Pdzk1"          "Gja5"           "Acp6"           "Tor1aip1"      
##  [9349] "Fmo5"           "Prkab2"         "Notch2"         "Adam30"        
##  [9353] "Gm12474"        "Vtcn1"          "Trim45"         "Igsf3"         
##  [9357] "Tspan2"         "Sike1"          "Axdnd1"         "Ampd1"         
##  [9361] "Bcas2"          "Syt6"           "Rhoc"           "4930564D02Rik" 
##  [9365] "Inka2"          "Adora3"         "Wdr77"          "Ovgp1"         
##  [9369] "Lrif1"          "Soat1"          "Kcna3"          "Kcna2"         
##  [9373] "Alx3"           "Eps8l3"         "Gnat2"          "Amigo1"        
##  [9377] "Taf13"          "Clcc1"          "Aknad1"         "Slc25a54"      
##  [9381] "Tor3a"          "Slc25a24"       "Gm9889"         "Dph5"          
##  [9385] "Extl2"          "Dbt"            "Sass6"          "Gm29736"       
##  [9389] "Plppr5"         "Dpyd"           "Alg14"          "Fam20b"        
##  [9393] "Cnn3"           "Gclm"           "Dnttip2"        "Bcar3"         
##  [9397] "Pde5a"          "Arln"           "Sec24d"         "Gm9372"        
##  [9401] "Gm22575"        "Ndst4"          "Ralgps2"        "Camk2d"        
##  [9405] "Zgrf1"          "Neurog2"        "Tifa"           "Elovl6"        
##  [9409] "Pla2g12a"       "Casp6"          "Col25a1"        "Lef1"          
##  [9413] "Papss1"         "Tex35"          "Ints12"         "Ppa2"          
##  [9417] "Cxxc4"          "Gm55241"        "Cenpe"          "Slc9b1"        
##  [9421] "Ube2d3"         "Manba"          "Slc39a8"        "Ppp3ca"        
##  [9425] "Micall1"        "Brinp2"         "Ddit4l"         "Dnajb14"       
##  [9429] "Trmt10a"        "Adh7"           "Adh1"           "Adh4"          
##  [9433] "Adh5"           "Eif4e"          "Mir1956"        "Kyat3"         
##  [9437] "Gm7430"         "Odf2l"          "Znhit6"         "Ddah1"         
##  [9441] "Gm6525"         "Bcl10"          "2410004B18Rik"  "Syde2"         
##  [9445] "Lpar3"          "Ssx2ip"         "Ctbs"           "4930562F07Rik" 
##  [9449] "Gng5"           "Ttll7"          "Gm5149"         "Fubp1"         
##  [9453] "Usp33"          "Zzz3"           "Pigk"           "Slc44a5"       
##  [9457] "Cryz"           "Lrriq3"         "Cacybp"         "Scp2-ps1"      
##  [9461] "Negr1"          "Zranb2"         "1810013D15Rik"  "Ankrd13c"      
##  [9465] "Gm22944"        "Gm6140"         "Pex2"           "Gm6194"        
##  [9469] "Hey1"           "Gpr52"          "Mrps28"         "Zfp704"        
##  [9473] "Gm17877"        "Zfand1"         "Snx16"          "Gm21631"       
##  [9477] "Rbis"           "Gm16399"        "Gm5150"         "Gm56811"       
##  [9481] "Zbtb37"         "Pde7a"          "Hps3"           "Gyg1"          
##  [9485] "Cpa3"           "Agtr1b"         "Naaladl2"       "Ect2"          
##  [9489] "Fndc3b"         "Actrt3"         "Lrrc31"         "Dars2"         
##  [9493] "4933429H19Rik"  "Phc3"           "Zmat3"          "Kcnmb3"        
##  [9497] "Gnb4"           "Mrpl47"         "Pex5l"          "Dnajc19"       
##  [9501] "Dcun1d1"        "Mccc1"          "Klhl20"         "Gm57858"       
##  [9505] "Qrfpr"          "Anxa5"          "Ccna2"          "Bbs7"          
##  [9509] "Cetn4"          "Nudt6"          "Ankrd50"        "1700017G19Rik" 
##  [9513] "Gm16508"        "Tex50"          "Sclt1"          "Ikzf5"         
##  [9517] "1700018B24Rik"  "Slc7a11"        "Elf2"           "Mgarp"         
##  [9521] "Maml3"          "Frem2"          "Ufm1"           "Exosc8"        
##  [9525] "4930558K02Rik"  "Ccna1"          "Nbea"           "Tm4sf1"        
##  [9529] "Wwtr1"          "Commd2"         "Gm6394"         "Siah2"         
##  [9533] "P2ry14"         "Igsf10"         "9330121J05Rik"  "Ssr3"          
##  [9537] "Dnm3"           "Gm8388"         "E130311K13Rik"  "Slc33a1"       
##  [9541] "Vmn2r-ps11"     "4931440P22Rik"  "Ccnl1"          "Lxn"           
##  [9545] "Rarres1"        "Gm8515"         "Snrpd2"         "Mettl13"       
##  [9549] "Gm17641"        "Ift80"          "Trim59"         "Kpna4"         
##  [9553] "B3galnt1"       "Zbbx"           "Wdr49"          "Golim4"        
##  [9557] "Gm5277"         "Rapgef2"        "Prrc2c"         "Etfdh"         
##  [9561] "Tmem144"        "Rbm46"          "Lrat"           "Gm10710"       
##  [9565] "Tlr2"           "Trim2"          "Fhdc1"          "Prss48"        
##  [9569] "Kirrel1"        "Fmo1"           "Ube2l3"         "Pear1"         
##  [9573] "Ntrk1"          "Prcc"           "Ttc24"          "Rhbg"          
##  [9577] "Bglap"          "Slc25a44"       "Sema4a"         "Lmna"          
##  [9581] "Fmo2"           "Lamtor2"        "Rxfp4"          "Gm10253"       
##  [9585] "Dap3"           "Rusc1"          "Mtx1"           "Mir92b"        
##  [9589] "Trim46"         "Slc50a1"        "Efna1"          "Mroh9"         
##  [9593] "Efna3"          "Efna4"          "Adam15"         "Zbtb7b"        
##  [9597] "Flad1"          "Cks1b"          "4632404H12Rik"  "Il6ra"         
##  [9601] "Gm24046"        "Creb3l4"        "Prrx1"          "Slc27a3"       
##  [9605] "Npr1"           "Gm23464"        "Lelp1"          "Sprr1b"        
##  [9609] "Sprr1a"         "Sprr4"          "Ivl"            "Lce1b"         
##  [9613] "Lce1e"          "Gorab"          "Lce1g"          "Lce1j"         
##  [9617] "Lce1k"          "Crct1"          "Lce1m"          "G430049J08Rik" 
##  [9621] "Riiad1"         "Tuft1"          "Psmb4"          "Psmd4"         
##  [9625] "Blzf1"          "Scnm1"          "Tnfaip8l2"      "Gabpb2"        
##  [9629] "Mllt11"         "Gm128"          "6330562C20Rik"  "Gm5070"        
##  [9633] "Adamtsl4"       "Ecm1"           "Tars2"          "Atp1b1"        
##  [9637] "Prpf3"          "Mrps21"         "Ciart"          "Gm20940"       
##  [9641] "Plekho1"        "Vps45"          "Bola1"          "H4c14"         
##  [9645] "Terc"           "BC107364"       "Huwe1"          "Xcl1"          
##  [9649] "Gm15441"        "Polr3gl"        "Rpl21-ps11"     "Nudt17"        
##  [9653] "Polr3c"         "Gpr89"          "Gja8"           "Bcl9"          
##  [9657] "Or13l2"         "Pde4dip"        "Tbx19"          "Phgdh"         
##  [9661] "Hsd3b3"         "Hsd3b6"         "Hsd3b1"         "Man1a2"        
##  [9665] "Ttf2"           "Ptgfrn"         "Cd2"            "Vangl1"        
##  [9669] "Sycp1"          "Sft2d2"         "Atg4a"          "Olfml3"        
##  [9673] "Dclre1b"        "Phtf1os"        "Magi3"          "Tafa3"         
##  [9677] "Mov10"          "Capza1"         "Cttnbp2nl"      "Kcnd3os"       
##  [9681] "Mpzl1"          "Rap1a"          "Cimap3"         "Cept1"         
##  [9685] "Cd53"           "Cym"            "Rbm15"          "Kcnc4"         
##  [9689] "Ubl4b"          "Strip1"         "Csf1"           "Pou2f1"        
##  [9693] "Gstm7"          "Gstm6"          "Gstm2"          "Gstm1"         
##  [9697] "Gstm4"          "Gnai3"          "Cyb561d1"       "Atxn7l2"       
##  [9701] "Gm12522"        "Celsr2"         "5330438I03Rik"  "Sars1"         
##  [9705] "Gpsm2"          "Stxbp3"         "Fndc7"          "Prpf38b"       
##  [9709] "Eeig2"          "Ntng1"          "Prmt6"          "Gm5548"        
##  [9713] "Amy1"           "Pogk"           "Rnpc3"          "A930005H10Rik" 
##  [9717] "Vcam1"          "Rtca"           "Trmt13"         "Mfsd14a"       
##  [9721] "Slc35a3"        "Agl"            "1700061I17Rik"  "Plppr4"        
##  [9725] "Uck2"           "Snx7"           "Rwdd3"          "Tlcd4"         
##  [9729] "Abcd3"          "Fnbp1l"         "Gm5981"         "Usp53"         
##  [9733] "Mettl14"        "Ndst3"          "1700006A11Rik"  "Gm56171"       
##  [9737] "1700003H04Rik"  "Ugt8a"          "Ank2"           "Larp7"         
##  [9741] "Alpk1"          "Ap1ar"          "Fam241a"        "Gm43656"       
##  [9745] "Egf"            "Gar1"           "Lrrc52"         "Sec24b"        
##  [9749] "Ostc"           "Rpl34"          "Gm5982"         "Hadh"          
##  [9753] "Sgms2"          "Aimp1"          "Gstcd"          "Nfkb1"         
##  [9757] "Cisd2"          "Fryl"           "Pbx1"           "Dapp1"         
##  [9761] "Mttp"           "4930579F01Rik"  "2410002F23Rik"  "Rap1gds1"      
##  [9765] "Gm4863"         "Gm6214"         "Pdha2"          "Bmpr1b"        
##  [9769] "Pdlim5"         "Gm5265"         "Lmo4"           "Hs2st1"        
##  [9773] "Ccn1"           "Dnai3"          "Rpf1"           "Rpl11"         
##  [9777] "Adgrl2"         "Ifi44l"         "Gipc2"          "Nexn"          
##  [9781] "Nuf2"           "Miga1"          "Msh4"           "Rabggtb"       
##  [9785] "Acadm"          "Lhx8"           "Cth"            "Srsf11"        
##  [9789] "Tgs1"           "Chchd7"         "Fam110b"        "Uap1"          
##  [9793] "Ubxn2b"         "Sdcbp"          "Gm11801"        "Chd7"          
##  [9797] "Clvs1"          "Gm12920"        "Cfap418"        "Gm11829"       
##  [9801] "Ccne2"          "Virma"          "Nos1ap"         "Rad54b"        
##  [9805] "Gem"            "Rbm12b2"        "Gm11841"        "Gm6793"        
##  [9809] "Triqk"          "Runx1t1"        "Nbn"            "Mmp16"         
##  [9813] "Cngb3"          "Atf6"           "Ttpa"           "Ggh"           
##  [9817] "Ccnc"           "Usp45"          "Pnisr"          "Coq3"          
##  [9821] "Faxc"           "Mms22l"         "Ndufaf4"        "Prdx6-ps2"     
##  [9825] "Dusp12"         "Gm11907"        "Epha7"          "Map3k7"        
##  [9829] "Bach2"          "Casp8ap2"       "Mdn1"           "Lyrm2"         
##  [9833] "Gm11942"        "Rragd"          "Srsf12"         "Fcrlb"         
##  [9837] "Rngtt"          "Akirin2"        "Rars2"          "1700009N14Rik" 
##  [9841] "Gm12384"        "Aco1"           "Smim27"         "Spink4"        
##  [9845] "Nfx1"           "Nudt2"          "Fcrla"          "Fam219aos"     
##  [9849] "Dnai1"          "4930578G10Rik"  "Phf24"          "Spata31g1"     
##  [9853] "Unc13b"         "Atp8b5"         "Rusc2"          "Creb3"         
##  [9857] "Rgp1"           "Uqcrb"          "Npr2"           "Serf2"         
##  [9861] "Tmem8b"         "Reck"           "Glipr2"         "Clta"          
##  [9865] "Melk"           "Zcchc7"         "Grhpr"          "1700055D18Rik" 
##  [9869] "G3bp2"          "Fcgr2b"         "Polr1e"         "Frmpd1"        
##  [9873] "Trmt10b"        "Dcaf10"         "Stra6l"         "Aldh1b1"       
##  [9877] "Ccdc180"        "Tmod1"          "Foxe1"          "Anp32b"        
##  [9881] "Fcgr3"          "Nans"           "Invs"           "Msantd3"       
##  [9885] "Tmeff1"         "Cavin4"         "Gm12452"        "Zfp189"        
##  [9889] "Rnf20"          "Cylc2"          "Gm12466"        "Sdhc"          
##  [9893] "Smc2"           "Toporsl"        "Gm12482"        "Or13f5"        
##  [9897] "Nipsnap3a"      "Nipsnap3b"      "Slc44a1"        "Fsd1l"         
##  [9901] "Fktn"           "Tal2"           "Pcp4l1"         "Tmem38b"       
##  [9905] "Zfp462"         "Actl7a"         "Abitram"        "Gm22300"       
##  [9909] "Pakap"          "Zkscan16"       "Gng10"          "Ugcg"          
##  [9913] "E130308A19Rik"  "Fcer1g"         "Snx30"          "Slc31a2"       
##  [9917] "Slc31a1"        "Prpf4"          "Bspry"          "4933430I17Rik" 
##  [9921] "Rgs3"           "Zfp618"         "Col27a1"        "Mir455"        
##  [9925] "Ndufs2"         "Orm2"           "Aknaos"         "Tmem268"       
##  [9929] "Pappa"          "Trim32"         "Gm11222"        "Gm11225"       
##  [9933] "Kdm4c"          "Gm11263"        "Snapc3"         "Usp21"         
##  [9937] "Cntln"          "Sh3gl2"         "Focad"          "Ifna5"         
##  [9941] "Ifna1"          "Mtap"           "Tgif2-ps1"      "Dmrta1"        
##  [9945] "Gm12643"        "Gm12644"        "Ufc1"           "Gm12653"       
##  [9949] "Tek"            "Fggy"           "Hook1"          "Nfia"          
##  [9953] "Patj"           "Gm55907"        "Atg4c"          "Gm10305"       
##  [9957] "Efcab7"         "B930036N10Rik"  "Pgm1"           "Ube2u"         
##  [9961] "Raver2"         "Dnajc6"         "Leprot"         "Dynlt5"        
##  [9965] "Mier1"          "Oma1"           "Dab1"           "Fyb2"          
##  [9969] "Ly9"            "Plpp3"          "Gm12727"        "Dhcr24"        
##  [9973] "Fam151a"        "Cdcp2"          "Ldlrad1"        "Ift25"         
##  [9977] "Ndc1"           "Glis1"          "Lrp8"           "Gm49712"       
##  [9981] "Slamf7"         "Magoh"          "Czib"           "Slc1a7"        
##  [9985] "Echdc2"         "Orc1"           "Kti12"          "Rab3b"         
##  [9989] "Calr4"          "Eps15"          "Ttc39a"         "Gm37065"       
##  [9993] "Faf1"           "Dmrta2"         "Bend5"          "Trabd2b"       
##  [9997] "Tal1"           "Pdzk1ip1"       "Gm12833"        "Efcab14"       
## [10001] "Mob3c"          "Kncn"           "Vangl2"         "Tmem275"       
## [10005] "Pomgnt1"        "Gm12950"        "Gpbp1l1"        "Ccdc163"       
## [10009] "Tesk2"          "Zswim5"         "Hectd3"         "Eif2b3"        
## [10013] "Ptch2"          "Timm23"         "Dynlt4"         "Gm25099"       
## [10017] "Gm23143"        "Tmem53"         "Hyi"            "Med8"          
## [10021] "Elovl1"         "D4Ertd617e"     "Slc2a1"         "Svbp"          
## [10025] "Pea15a"         "Cldn19"         "Gm12957"        "Hivep3"        
## [10029] "Scmh1"          "Slfnl1"         "Cited4"         "Rims3"         
## [10033] "Col9a2"         "Trit1"          "Gm12901"        "Casq1"         
## [10037] "Rhbdl2"         "Mycbp"          "Pou3f1"         "Fhl3"          
## [10041] "Sf3a3"          "Mir697"         "Inpp5b"         "Epha10"        
## [10045] "Airim"          "Rspo1"          "Atp1a2"         "Gnl2"          
## [10049] "Snip1"          "Grik3"          "Mrps15"         "Oscp1"         
## [10053] "Stk40"          "Eva1b"          "Gm12945"        "Clspn"         
## [10057] "5730409E04Rik"  "Kcnj9"          "Psmb2"          "Zmym6"         
## [10061] "Tmem35b"        "Dlgap3"         "Csmd2"          "A3galt2"       
## [10065] "Trim62"         "Ak2"            "Rnf19b"         "Fndc5"         
## [10069] "Gm2710"         "Yars1"          "Sync"           "Zbtb8os"       
## [10073] "Gm24621"        "Bsdc1"          "Marcksl1"       "Ptp4a2"        
## [10077] "Spocd1"         "Adgrb2"         "Pef1"           "Fh1"           
## [10081] "Fabp3"          "Laptm5"         "Mecr"           "Srsf4"         
## [10085] "Tmem200b"       "Gm10300"        "Snora16a"       "Dnajc8"        
## [10089] "Ptafr"          "Wasf2"          "Cic"            "Opn3"          
## [10093] "Cd164l2"        "Map3k6"         "Slc9a1"         "Gpatch3"       
## [10097] "Ubxn11"         "Slc30a2"        "Gm5589"         "Pafah2"        
## [10101] "Paqr7"          "Aunip"          "Chml"           "Rsrp1"         
## [10105] "Syf2"           "Stpg1"          "Il22ra1"        "Myom3"         
## [10109] "Srsf10"         "Fuca1"          "Hmgcl"          "Gale"          
## [10113] "Gm13007"        "Rbm8a2"         "Tcea3"          "Luzp1"         
## [10117] "Tex46"          "Lactbl1"        "Wnt4"           "1700013G24Rik" 
## [10121] "Hspg2"          "Ece1"           "Sh2d5"          "Kif17"         
## [10125] "Cep170"         "AB041806"       "Mul1"           "Camk2n1"       
## [10129] "Pla2g2c"        "Pla2g2d"        "Pla2g2a"        "Pla2g2e"       
## [10133] "Akr7a5"         "Aldh4a1"        "Rcc2"           "Akt3"          
## [10137] "Sdhb"           "Mfap2"          "Spata21"        "Fbxo42"        
## [10141] "Arhgef19"       "Epha2"          "Fam131c"        "Hspb7"         
## [10145] "Zbtb17"         "B330016D10Rik"  "Hnrnpu"         "AI507597"      
## [10149] "Agmat"          "Gm13038"        "Pramel1"        "Pramel12"      
## [10153] "Aadacl4fm1"     "Gm13127"        "Dhrs3"          "Zfp985"        
## [10157] "Zfp600"         "Smyd3"          "Zfp991"         "Zfp982"        
## [10161] "Fv1"            "2510039O18Rik"  "Mthfr"          "Mad2l2"        
## [10165] "Mtor"           "Exosc10"        "Srm"            "Casz1"         
## [10169] "Coq8a"          "Dffa"           "Lzic"           "Slc2a7"        
## [10173] "Eno1"           "Rere"           "Tnfrsf9"        "Gm23405"       
## [10177] "Dnajc11"        "Hes2"           "Rpl22"          "Psen2"         
## [10181] "Chd5"           "Cep104"         "Megf6"          "B230104I21Rik" 
## [10185] "Ttc34"          "Mmel1"          "Hes5"           "Gm10564"       
## [10189] "Morn1"          "Faap20"         "Gm5069"         "Cfap74"        
## [10193] "Gnb1"           "Cdk11b"         "Fndc10"         "Ssu72"         
## [10197] "Mrpl20"         "Ccnl2"          "Aurkaip1"       "Mxra8"         
## [10201] "Dvl1"           "Gm38164"        "Stum"           "Ints11"        
## [10205] "Acap3"          "Sdf4"           "Tnfrsf4"        "9430015G10Rik" 
## [10209] "Rnf223"         "Tmem68"         "Rps20"          "Bpnt2"         
## [10213] "Nsmaf"          "Mixl1"          "Asph"           "4930448K20Rik" 
## [10217] "Gm11814"        "Plekhf2"        "Ints8"          "Dpy19l4"       
## [10221] "Esrp1"          "Tmem67"         "Cibar1"         "Slc26a7"       
## [10225] "Ephx1"          "Lrrc69"         "Otud6b"         "Decr1"         
## [10229] "Osgin2"         "Ripk2"          "Cnbd1"          "Cpne3"         
## [10233] "Wwp1"           "Nkain3"         "Prdm13"         "Ccdc121rt1"    
## [10237] "Tstd3"          "4930528A17Rik"  "Pou3f2"         "Klhl32"        
## [10241] "Fhl5"           "Ufl1"           "Gm11895"        "Manea"         
## [10245] "Pnrc1"          "Spaca1"         "Lbr"            "Orc3"          
## [10249] "Gm136"          "Smim8"          "Mob3b"          "C9orf72"       
## [10253] "Gm12369"        "Gm12387"        "Rigi"           "Topors"        
## [10257] "Ndufb6"         "Degs1"          "Aptx"           "Bag1"          
## [10261] "Aqp7"           "Aqp3"           "Nol6"           "Kif24"         
## [10265] "Myorg"          "Spmip6"         "Enho"           "Cntfr"         
## [10269] "Capn2"          "Dctn3"          "Sigmar1"        "Fancg"         
## [10273] "Pigo"           "Stoml2"         "Atosb"          "Rmrp"          
## [10277] "Tpm2"           "Tln1"           "Gba2"           "Ccdc185"       
## [10281] "Msmp"           "Spag8"          "Fam221b"        "Or13e8"        
## [10285] "Or13c7d"        "Gne"            "Gm56267"        "Pax5"          
## [10289] "Zbtb5"          "Shb"            "1700056E22Rik"  "Tstd2"         
## [10293] "Xpa"            "Trmo"           "Trim14"         "Tbc1d2"        
## [10297] "Gm568"          "Alg2"           "Mrpl50"         "Pgap4"         
## [10301] "Ppp3r2"         "Hlx"            "Abca1"          "Mexis"         
## [10305] "Gm12513"        "Actl7b"         "Ctnnal1"        "Tmem245"       
## [10309] "Frrs1l"         "Epb41l4b"       "Ptpn3"          "Gm12526"       
## [10313] "Tbl3"           "Tmem234"        "Mtarc2"         "D630039A03Rik" 
## [10317] "Txn1"           "Or2k2"          "Ptgr1"          "Shoc1"         
## [10321] "Inip"           "Gm12542"        "Zfp37"          "Cdc26"         
## [10325] "Wdr31"          "C130074G19Rik"  "Alad"           "Ambp"          
## [10329] "Akna"           "Tex48"          "Tnfsf15"        "Hmgb1-rs18"    
## [10333] "Gm11224"        "Megf9"          "Rasef"          "Dmac1"         
## [10337] "Iars2"          "Mpdz"           "Nfib"           "Zdhhc21"       
## [10341] "Frem1"          "Ttc39b"         "Psip1"          "Bnc2"          
## [10345] "Haus6"          "Plin2"          "Mllt3"          "9630028B13Rik" 
## [10349] "Ifna14"         "Mrpl48"         "Ifna2"          "Gm13274"       
## [10353] "Elavl2"         "Gm12669"        "Izumo3"         "Gm12642"       
## [10357] "Tusc1"          "Gm23443"        "Gm9722"         "Caap1"         
## [10361] "Plaa"           "Eqtn"           "Mysm1"          "Jun"           
## [10365] "Gm12695"        "Gm12696"        "Tm2d1"          "Itgb3bp"       
## [10369] "Ccdc50-ps"      "Lyplal1"        "Jak1"           "Gm12799"       
## [10373] "Insl5"          "4921539E11Rik"  "Prkaa2"         "Gm12722"       
## [10377] "Pcsk9"          "Cimap2"         "Ttc4"           "Mroh7"         
## [10381] "Rrp15"          "Tceanc2"        "Lrrc42"         "Lrp8os1"       
## [10385] "Cpt2"           "Podn"           "Scp2"           "Zyg11b"        
## [10389] "Shisal2a"       "Prpf38a"        "Rnf11"          "Kctd3"         
## [10393] "4930522H14Rik"  "Cdkn2c"         "Gm55392"        "Rpl3"          
## [10397] "Foxe3"          "Cmpk1"          "Dmbx1"          "Nsun4"         
## [10401] "Uqcrh"          "Lurap1"         "Kcnk2"          "Tspan1"        
## [10405] "Llph"           "Tmem69"         "Mmachc"         "Toe1"          
## [10409] "Hpdl"           "Dmap1"          "Klf17"          "Dph2"          
## [10413] "Artn"           "Cenpf"          "St3gal3"        "Kdm4a"         
## [10417] "Szt2"           "Cdc20"          "Mpl"            "Ccnb1"         
## [10421] "Gm12865"        "Zfp691"         "Ermap"          "Tmem269"       
## [10425] "Wars1"          "Smyd2"          "AU022252"       "Ccdc30"        
## [10429] "Ppcs"           "Guca2b"         "Ctps1"          "Mir30c-1"      
## [10433] "Exo5"           "Zfp69"          "Smap2"          "Zmpste24"      
## [10437] "Vash2"          "Tmco2"          "Rlf"            "Gm12877"       
## [10441] "Cap1"           "Gm17244"        "Ppie"           "Oxct2a"        
## [10445] "Ndufs5"         "Akirin1"        "D130007C19Rik"  "Flvcr1"        
## [10449] "Utp11"          "Cdca8"          "Dnali1"         "Sh3d21"        
## [10453] "Map7d1"         "Tekt2"          "Ago3"           "Ago1"          
## [10457] "Tfap2e"         "Rps28"          "Tatdn3"         "Gja4"          
## [10461] "Gjb3"           "CK137956"       "Hmgb4"          "Zscan20"       
## [10465] "Zfp362"         "Hpca"           "S100pbp"        "Nhsl3"         
## [10469] "Rbbp4"          "Garin4"         "Hdac1"          "Lck"           
## [10473] "Fam167b"        "Eif3i"          "Iqcc"           "Txlna"         
## [10477] "Tmem39b"        "Khdrbs1"        "Tinagl1"        "Ldc1"          
## [10481] "Nenf"           "Serinc2"        "Gm10570"        "Zcchc17"       
## [10485] "Epb41"          "Oprd1"          "Gmeb1"          "Trnau1ap"      
## [10489] "Rcc1"           "Snora73b"       "Snora73a"       "1700034H15Rik" 
## [10493] "Phactr4"        "Med18"          "Sesn2"          "Atp5if1"       
## [10497] "Xkr8"           "Smpdl3b"        "Themis2"        "Stx12"         
## [10501] "Fam76a"         "Gpr3"           "Traf5"          "Tmem222"       
## [10505] "Trnp1"          "Nudc"           "Gm25270"        "Rps6ka1"       
## [10509] "Dhdds"          "Lin28a"         "Sh3bgrl3"       "Cep85"         
## [10513] "Catsper4"       "Hhat"           "Zfp593"         "Fam110d"       
## [10517] "Extl1"          "Man1c1"         "Tmem50a"        "Srrm1"         
## [10521] "Gm12990"        "Nipal3"         "Grhl3"          "Pnrc2"         
## [10525] "Sertad4"        "Lypla2"         "Pithd1"         "Eloa"          
## [10529] "C1qb"           "C1qc"           "C1qa"           "Cdc42"         
## [10533] "Alpl"           "Pink1"          "Cda"            "Anapc2"        
## [10537] "Syt14"          "Vwa5b1"         "Pla2g2f"        "Pla2g5"        
## [10541] "Otud3"          "Gm16287"        "Mrto4"          "Igsf21"        
## [10545] "Gm9867"         "Arhgef10l"      "Padi6"          "G0s2"          
## [10549] "Padi3"          "Crocc"          "Necap2"         "Clcnka"        
## [10553] "Clcnkb"         "Spen"           "Tmem82"         "Slc25a34"      
## [10557] "Plekhm2"        "Dnajc16"        "Cr1l"           "Cela2a"        
## [10561] "Ctrc"           "Fhad1"          "Kazn"           "Prdm2"         
## [10565] "Gm13042"        "Trappc2"        "Pramel5"        "Pramel13"      
## [10569] "Cfap107"        "Cnksr3"         "Tnfrsf1b"       "Tnfrsf8"       
## [10573] "Gm13229"        "Rps19-ps3"      "Zfp933"         "Miip"          
## [10577] "Plod1"          "Clcn6"          "Agtrap"         "Fbxo6"         
## [10581] "Syne1"          "Fbxo44"         "Disp3"          "Ubiad1"        
## [10585] "Angptl7"        "Tardbp"         "Cort"           "Rpsa-ps12"     
## [10589] "Pgd"            "Kif1b"          "Rbp7"           "Zbtb2"         
## [10593] "Nmnat1"         "Slc25a33"       "Spsb1"          "H6pd"          
## [10597] "Car6"           "Gm13092"        "Vamp3"          "Phf13"         
## [10601] "Gm9768"         "Zbtb48"         "Lrp11"          "Espn"          
## [10605] "Hes3"           "Rnf207"         "Ajap1"          "BC049688"      
## [10609] "Smim1"          "Ccdc27"         "Trp73"          "5930403L14Rik" 
## [10613] "Actrt2"         "Nup43"          "Prxl2b"         "Tnfrsf14"      
## [10617] "Plch2"          "Rer1"           "Prkcz"          "Gm13171"       
## [10621] "1500002C15Rik"  "Atad3a"         "Tmem88b"        "Mxra8os"       
## [10625] "Katna1"         "Tas1r3"         "Cptp"           "Gm16008"       
## [10629] "Ttll10"         "Agrn"           "Cdk6"           "Fam133b"       
## [10633] "1700109H08Rik"  "Akap9"          "Gm38697"        "Ppil4"         
## [10637] "Tex47"          "Gm8802"         "Steap4"         "Sri"           
## [10641] "Abcb1a"         "Abcb4"          "Tmem243"        "Elapor2"       
## [10645] "Gm6641"         "Speer3"         "Ddx24"          "Gm25682"       
## [10649] "Sema3e"         "Pclo"           "Cacna2d1"       "Speer4f1"      
## [10653] "Sema3c"         "Magi2"          "Tmem60"         "Fgl2"          
## [10657] "Fam185a"        "Armc10"         "Gm23680"        "Pmpcb"         
## [10661] "Psmc2"          "Kmt2e"          "Gm9836"         "Nos3"          
## [10665] "Abcb8"          "Agap3"          "1700022A21Rik"  "Nub1"          
## [10669] "1500035N22Rik"  "Sf3b5"          "Dpp6"           "Rbm33"         
## [10673] "Nom1"           "Dnajb6"         "Selenoi"        "Drc1"          
## [10677] "Cimip2c"        "Kcnk3"          "Slc35f6"        "Cenpa"         
## [10681] "Plagl1"         "Dpysl5"         "Emilin1"        "Abhd1"         
## [10685] "Tcf23"          "Atraid"         "Dnajc5g"        "Trim54"        
## [10689] "Snx17"          "Nrbp1"          "Krtcap3"        "Fuca2"         
## [10693] "Zfp512"         "Ccdc121"        "Gpn1"           "Slc4a1ap"      
## [10697] "Mrpl33"         "Babam2"         "Fosl2"          "Plb1"          
## [10701] "Ppp1cb"         "Ywhah"          "Adat2"          "Maea"          
## [10705] "Uvssa"          "Gm10459"        "Rps29"          "Nsd2"          
## [10709] "Nicol1"         "Rnf4"           "Fam193a"        "Sh3bp2"        
## [10713] "Add1"           "Nmbr"           "Grk4"           "Htt"           
## [10717] "Msantd1"        "Rgs12"          "Adra2c"         "Hmx1"          
## [10721] "Plk-ps1"        "Ablim2"         "Afap1"          "Grpel1"        
## [10725] "Cited2"         "Jakmip1"        "Gm1043"         "Crmp1"         
## [10729] "Evc2"           "Cytl1"          "Stx18"          "Tmem128"       
## [10733] "Otop1"          "Drd5"           "Dnaja1"         "Txlnb"         
## [10737] "Cir1"           "Gm16401"        "Gm42984"        "4930431F12Rik" 
## [10741] "Lap3"           "Slit2"          "Gm40319"        "Sod3"          
## [10745] "Anapc4"         "Smim20"         "Gm10827"        "Tbc1d19"       
## [10749] "Stim2"          "Pcdh7"          "Gm6632"         "G6pd2"         
## [10753] "Nwd2"           "Pgcka1"         "Klf3"           "Fam114a1"      
## [10757] "Klhl5"          "Rab14"          "Nhsl1"          "Klb"           
## [10761] "Lias"           "Uchl1"          "Limch1"         "Gm6517"        
## [10765] "Tmem33"         "Slc30a9"        "C330024D21Rik"  "Gm5867"        
## [10769] "Guf1"           "Tpi-rs5"        "Atp10d"         "Ociad1"        
## [10773] "Gm34583"        "Rasl11b"        "Pdgfra"         "Kit"           
## [10777] "Srd5a3"         "Gm7467"         "Cep135"         "Cracd"         
## [10781] "Ifngr1"         "Paics"          "Arl9"           "Rest"          
## [10785] "Adgrl3"         "Hmgn2"          "Csn1s1"         "Gm7337"        
## [10789] "BC051076"       "Cabs1"          "Gm7721"         "Il20ra"        
## [10793] "Utp3"           "Rufy3"          "Mob1b"          "Dck"           
## [10797] "Gm9958"         "Pf4"            "Cxcl3"          "Cxcl1"         
## [10801] "Mthfd2l"        "Areg"           "Map3k5"         "Parm1"         
## [10805] "Thap6"          "Uso1"           "Art3"           "Fam47e"        
## [10809] "Shroom3"        "Gm6450"         "Gm22915"        "Septin11"      
## [10813] "Ccng2"          "Rpl32l"         "Gm25937"        "Cxcl13"        
## [10817] "Mrpl1"          "Anxa3"          "Bmp2k"          "Gm8048"        
## [10821] "Fgf5"           "Bmp3"           "Gm16226"        "Enoph1"        
## [10825] "Mtfr2"          "Cops4"          "Mrps18c"        "Gpat3"         
## [10829] "Arhgap24"       "Ptpn13"         "Aff1"           "Nudt9"         
## [10833] "Dmp1"           "Thoc2l"         "Lrrc8c"         "Gm2467"        
## [10837] "Zfp326"         "Cdc7"           "n-R5s173"       "Btbd8"         
## [10841] "Rpap2"          "Mtf2"           "Ccdc18"         "Pigg"          
## [10845] "Pcgf3"          "Idua"           "Aldh8a1"        "Fgfrl1"        
## [10849] "Plcxd1"         "Golga3"         "Gm42596"        "Ddx51"         
## [10853] "Ttc28"          "Pitpnb"         "Crybb1"         "Tfip11"        
## [10857] "Hps4"           "1700021A07Rik"  "Ccdc121rt2"     "Aym1"          
## [10861] "Wscd2"          "Usp30"          "Ung"            "Acacb"         
## [10865] "Ube3b"          "Fam222a"        "Tchp"           "4930519G04Rik" 
## [10869] "Pabpn1"         "1700020N01Rik"  "Oasl2"          "Oasl1"         
## [10873] "2210016L21Rik"  "Sppl3"          "Coq5"           "Srsf9"         
## [10877] "Triap1"         "Msi1"           "Pla2g1b"        "Pxn"           
## [10881] "Sgk1"           "Rplp0"          "Gcn1"           "Rab35"         
## [10885] "Cit"            "Taok3"          "Vsig10"         "Wsb2"          
## [10889] "Gm9754"         "Hrk"            "Tbx5"           "Gm10825"       
## [10893] "Rbm19"          "Slc8b1"         "Iqcd"           "Ddx54"         
## [10897] "Rasal1"         "Hectd4"         "Brap"           "Atxn2"         
## [10901] "Pptc7"          "Vps29"          "Slc2a12"        "Gpn3"          
## [10905] "Arpc3"          "Anapc7"         "P2rx4"          "A930024E05Rik" 
## [10909] "Tmem120b"       "Gm38102"        "Setd1b"         "Cfap251"       
## [10913] "Mlxip"          "Gm37416"        "Lrrc43"         "Kntc1"         
## [10917] "Denr"           "Ccdc62"         "Hip1r"          "Arl6ip4"       
## [10921] "Kmt5a"          "Snrnp35"        "Tmed2"          "Ddx55"         
## [10925] "Slc18b1"        "Gtf2h3"         "Atp6v0a2"       "Dnah10"        
## [10929] "Zfp664"         "Rflna"          "Gm10382"        "Bri3bp"        
## [10933] "Aacs"           "Tmem132b"       "Tmem132c"       "Taar7b"        
## [10937] "Glt1d1"         "Fzd10"          "Ran"            "Adgrd1"        
## [10941] "Sfswap"         "Mmp17"          "Mrps17"         "Nipsnap2"      
## [10945] "Cct6a"          "Zbed5"          "Stx7"           "Nupr2"         
## [10949] "Crcp"           "Tpst1"          "Kctd7"          "Tyw1"          
## [10953] "Gtf2ird2"       "Rfc2"           "Gm10369"        "Mettl27"       
## [10957] "Cldn3"          "Ccn2"           "Abhd11"         "Stx1a"         
## [10961] "Dnajc30"        "Mlxipl"         "Tbl2"           "Bcl7b"         
## [10965] "Nsun5"          "Rhbdd2"         "Por"            "Srrm3"         
## [10969] "Gm4777"         "Hspb1"          "Dtx2"           "Upk3b"         
## [10973] "Upk3bl"         "Rasa4"          "Polr2j"         "Alkbh4"        
## [10977] "Myl10"          "Fis1"           "Cldn15"         "Nmt1"          
## [10981] "Epb41l2"        "Plod3"          "Actl6b"         "Lrch4"         
## [10985] "Tsc22d4"        "Ppp1r35"        "Zcwpw1"         "Smok3c"        
## [10989] "Zkscan1"        "Zscan21"        "Cops6"          "Arhgap18"      
## [10993] "Ap4m1"          "Cnpy4"          "Mblac1"         "Lamtor4"       
## [10997] "Pvrig"          "Gm10874"        "Zfp157"         "A430033K04Rik" 
## [11001] "Fam20c"         "Foxl3"          "Ptprk"          "6330403L08Rik" 
## [11005] "Dnaaf5"         "Sun1"           "Get4"           "Gper1"         
## [11009] "Mafk"           "Elfn1"          "Nudt1"          "Eif3b"         
## [11013] "Amz1"           "Pebp1"          "Gm26970"        "Foxk1"         
## [11017] "Wipi2"          "Slc29a4"        "Spdye4b"        "Zfp12"         
## [11021] "Daglb"          "Fam220a"        "Cyth3"          "Pms2"          
## [11025] "Mtcl3"          "Bhlha15"        "Bri3"           "Nptx2"         
## [11029] "Trrap"          "1700018F24Rik"  "Arpc1b"         "Bud31"         
## [11033] "Cpsf4"          "Zkscan5"        "Zscan25"        "Echdc1"        
## [11037] "Cdk8"           "Wasf3"          "Gtf3a"          "Polr1d"        
## [11041] "Gsx1"           "Pdx1"           "Gm6054"         "Pomp"          
## [11045] "Mtus2"          "Alox5ap"        "Hddc2"          "Tex26"         
## [11049] "Wdr95"          "Fry"            "Brca2"          "Rbm48"         
## [11053] "Gatad1"         "Fzd1"           "Cdk14"          "Cldn12"        
## [11057] "Steap2"         "Trdn"           "Steap1"         "Gm5714"        
## [11061] "Gm24525"        "Adam22"         "Rundc3b"        "Crot"          
## [11065] "Dmtf1"          "4930568A13Rik"  "Cd36"           "Gnai1"         
## [11069] "Tspyl1"         "Rsbn1l"         "Ptpn12"         "Rpl31-ps21"    
## [11073] "Ccdc146"        "Fbxl13"         "Napepld"        "Dnajc2"        
## [11077] "Reln"           "Orc5"           "Gm15421"        "Tspyl4"        
## [11081] "5031425E22Rik"  "Tomm7"          "Gabarapl2"      "Kcnh2"         
## [11085] "Atg9b"          "Cdk5"           "Tmub1"          "Asb10"         
## [11089] "Iqca1l"         "Smarcd3"        "Rps27"          "Gstm3"         
## [11093] "Rheb"           "E130116L18Rik"  "Kmt2c"          "Gm10062"       
## [11097] "Xrcc2"          "Speer4a1"       "4930584F24Rik"  "Speer4b"       
## [11101] "Shh"            "Lmbr1"          "Hdac2"          "Cib4"          
## [11105] "Gm9899"         "Ost4"           "Cgref1"         "Slc5a6"        
## [11109] "Ucn"            "Mpv17"          "Eif2b4"         "Gm9970"        
## [11113] "Ift172"         "Lama4"          "Gm40275"        "Rbks"          
## [11117] "Gm10461"        "Prr14l"         "Nkx1-1"         "G630022F23Rik" 
## [11121] "Letm1"          "Haus3"          "Tnip2"          "Mfsd10"        
## [11125] "Tube1"          "Nop14"          "Lrpap1"         "Cpz"           
## [11129] "Trmt44"         "4931431C16Rik"  "Htra3"          "2210406O10Rik" 
## [11133] "Tbc1d14"        "D5Ertd579e"     "Bloc1s4"        "Fyn"           
## [11137] "Man2b2"         "Stk32b"         "Zbtb49"         "Slc2a9"        
## [11141] "Wdr1"           "Zfp518b"        "Gm43806"        "Rab28"         
## [11145] "Nkx3-2"         "Bod1l"          "Gm8055"         "Gm5298"        
## [11149] "Gm7181"         "Gm5554"         "Gm7854"         "Prom1"         
## [11153] "Tapt1"          "D5Ertd615e"     "Qdpr"           "Fam184b"       
## [11157] "Lcorl"          "Mettl24"        "Kcnip4"         "Ccdc149"       
## [11161] "8030423F21Rik"  "Arap2"          "Nwd2os"         "Rell1"         
## [11165] "Gm43840"        "Gm20033"        "Tmem156"        "Ugdh"          
## [11169] "Wasf1"          "Smim14"         "Rbm47"          "Gm15794"       
## [11173] "Atp8a1"         "Kctd8"          "Gnpda2"         "Cox7b2"        
## [11177] "Commd8"         "Corin"          "Nfxl1"          "Ak9"           
## [11181] "Zar1"           "Txk"            "Gm9870"         "Slain2"        
## [11185] "Lrrc66"         "Chic2"          "Clock"          "Pdcl2"         
## [11189] "A730089K16Rik"  "Aasdh"          "Mical1"         "Ppat"          
## [11193] "Noa1"           "Igfbp7"         "Pea15b-ps"      "Cenpc1"        
## [11197] "Uba6"           "Tmprss11c"      "Sult1e1"        "Csn2"          
## [11201] "Grsf1"          "Naa60"          "Sesn1"          "Mkrn1-ps1"     
## [11205] "Gc"             "Adamts3"        "Rchy1"          "Cdkl2"         
## [11209] "Ppef2"          "Naaa"           "Cxcl11"         "Nup54"         
## [11213] "Scarb2"         "Snx3"           "Ccdc158"        "Paqr3"         
## [11217] "Gk2"            "Antxr2"         "A730035I17Rik"  "1700010H22Rik" 
## [11221] "Rasgef1b"       "Hnrnpd"         "Hnrnpdl"        "Tmem150c"      
## [11225] "Ostm1"          "Gm8091"         "Gm19620"        "Plac8"         
## [11229] "Coq2"           "Hpse"           "Abraxas1"       "Nkx6-1"        
## [11233] "Wdfy3"          "Mapk10"         "Klhl8"          "Sec63"         
## [11237] "Hsd17b11"       "Sparcl1"        "Zfp951"         "Gbp8"          
## [11241] "Gbp4"           "Rps15a"         "Gm19566"        "Barhl2"        
## [11245] "Hfm1"           "Tgfbr3"         "Bend3"          "Gfi1"          
## [11249] "Evi5"           "Dipk1a"         "Tmed5"          "Atp5me"        
## [11253] "Slc49a3"        "Cplx1"          "Gak"            "Rnf212"        
## [11257] "Gm8508"         "Cd24a"          "AB010352"       "Gtpbp6"        
## [11261] "5930411N13Rik"  "Pgam5"          "Pxmp2"          "P2rx2"         
## [11265] "Fbrsl1"         "Noc4l"          "Gm22716"        "Pus1"          
## [11269] "F930017D23Rik"  "Ulk1"           "Hscb"           "E130006D01Rik" 
## [11273] "Srrd"           "Ccdc121rt3"     "Sez6l"          "Myo18b"        
## [11277] "Grk3"           "Crybb2"         "Crybb3"         "Gm9034"        
## [11281] "2900026A02Rik"  "F830115B05Rik"  "Cmklr1"         "Sart3"         
## [11285] "Selplg"         "Coro1c"         "Ssh1"           "Alkbh2"        
## [11289] "Foxn4"          "Kctd10"         "Rtn4ip1"        "Trpv4"         
## [11293] "Gltp"           "Git2"           "4930515G01Rik"  "2610524H06Rik" 
## [11297] "Ywhaq-ps2"      "Hnf1a"          "Acads"          "Unc119b"       
## [11301] "Mlec"           "Gm5950"         "Gatc"           "Cox6a1"        
## [11305] "4930430O22Rik"  "Sirt4"          "1110006O24Rik"  "Bicdl1"        
## [11309] "Ccdc60"         "Srrm4"          "Suds3"          "Gm10399"       
## [11313] "Hp1bp3"         "Gm6983"         "Rfc5"           "Fbxw8"         
## [11317] "Rnft2"          "Sdsl"           "Plbd2"          "Gm43579"       
## [11321] "Dtx1"           "Rph3a"          "Ptpn11"         "Trafd1"        
## [11325] "Prep"           "Erp29"          "Adam1b"         "Adam1a"        
## [11329] "Mapkapk5"       "Aldh2"          "Acad10"         "Cux2"          
## [11333] "Ccdc63"         "Tctn1"          "Rad9b"          "Popdc3"        
## [11337] "Gm10064"        "Anapc5"         "Kdm2b"          "Morn3"         
## [11341] "Il31"           "Diablo"         "Clip1"          "Zcchc8"        
## [11345] "Rsrc2"          "Vps37b"         "Popdc1"         "Abcb9"         
## [11349] "Pitpnm2"        "Rilpl1"         "Eif2b1"         "Ccdc92"        
## [11353] "Ncor2"          "Scarb1"         "Dhx37"          "Gm7774"        
## [11357] "Slc15a4"        "Vgll2"          "Fzd10os"        "Rimbp2"        
## [11361] "Stx2"           "Septin14"       "Gusb"           "Asl"           
## [11365] "Sbds"           "A330070K13Rik"  "Galnt17"        "Auts2"         
## [11369] "Dcbld1"         "Ncf1"           "Gtf2ird1"       "Clip2"         
## [11373] "Lat2"           "Eif4h"          "Eln"            "Tmem270"       
## [11377] "Cldn13"         "Cldn4"          "Wbscr25"        "Nus1"          
## [11381] "Vps37d"         "Fzd9"           "Pom121"         "Hip1"          
## [11385] "Tmem120a"       "Styxl1"         "Ssc4d"          "Gm56207"       
## [11389] "Lrwd1"          "Prkrip1"        "Pln"            "Gm5050"        
## [11393] "Cux1"           "Znhit1"         "Ap1s1"          "Serpine1"      
## [11397] "Trim56"         "Slc12a9"        "Zan"            "Mospd3"        
## [11401] "Pcolce"         "Tmem229b"       "Agfg2"          "Zfp113"        
## [11405] "Mir25"          "Mir93"          "Taf6"           "Trappc14"      
## [11409] "Gpc2"           "1700123K08Rik"  "Zfp68"          "Pdgfa"         
## [11413] "Asf1a"          "Adap1"          "Chlsn"          "4930432F04Rik" 
## [11417] "Zfand2a"        "Ints1"          "Tmem184a"       "Psmg3"         
## [11421] "Mad1l1"         "Snx8"           "Grifin"         "Rnf220"        
## [11425] "Dpm2"           "Msl3l2"         "Ttyh3"          "Iqce"          
## [11429] "Gna12"          "Card11"         "Papolb"         "Mmd2"          
## [11433] "Tnrc18"         "Gm15770"        "Or10ah1-ps1"    "Gm7291"        
## [11437] "Smpdl3a"        "Rbakdn"         "Rbak"           "Spdye4a"       
## [11441] "Ints15"         "Rac1"           "Ankrd61"        "Ccz1"          
## [11445] "Tecpr1"         "Baiap2l1"       "Tmem130"        "Gcc2"          
## [11449] "Gm4871"         "Pdap1"          "Ptcd1"          "Atp5mf"        
## [11453] "Zkscan14"       "1700001J03Rik"  "Rnf6"           "Usp12"         
## [11457] "Mtif3"          "Lnx2"           "Ccdc138"        "Flt3"          
## [11461] "Flt1"           "Slc46a3"        "Gm10167"        "Slc7a1"        
## [11465] "Katnal1"        "Hmgb1"          "Zar1l"          "N4bp2l2"       
## [11469] "Stard13"        "Sh3rf3"         "Rfc3"           "Zfp788"        
## [11473] "Vmn2r-ps54"     "Gm2651"         "Vps50"          "Col1a2"        
## [11477] "Casd1"          "Ppp1r9a"        "Asb4"           "Dync1i1"       
## [11481] "Sowahc"         "Dlx6"           "Sdhaf3"         "Tac1"          
## [11485] "C1galt1"        "Mios"           "Nxph1"          "Phf14"         
## [11489] "Gm54938"        "Hormad1"        "Tmem106b"       "P4ha1"         
## [11493] "Foxp2"          "Tes"            "Cav1"           "Capza2"        
## [11497] "St7"            "Cftr"           "Lsm8"           "Ankrd7"        
## [11501] "Cped1"          "Wnt16"          "Gm10322"        "Asb15"         
## [11505] "Lmod2"          "Spam1"          "6530409C15Rik"  "Snd1"          
## [11509] "Mir129-1"       "Hilpda"         "Calu"           "Ccdc136"       
## [11513] "Flnc"           "Micu1"          "Irf5"           "Tspan33"       
## [11517] "Smo"            "Smkr-ps"        "Nrf1"           "Cpa1"          
## [11521] "Mest"           "Mir335"         "Mkln1"          "1700012A03Rik" 
## [11525] "Ascc1"          "Akr1b8"         "Akr1b10"        "Akr1b7"        
## [11529] "Bpgm"           "Cald1"          "Agbl3"          "Stra8"         
## [11533] "Akr1d1"         "Atp6v0c"        "Tmem213"        "Golm1"         
## [11537] "Spock2"         "Gm7504"         "Ift56"          "Luc7l2"        
## [11541] "Clec2l"         "Tbxas1"         "4930599N23Rik"  "Ndufb2"        
## [11545] "Tmem178b"       "Prss2"          "Try4"           "Vsir"          
## [11549] "Try10"          "Prss1l"         "Gm5409"         "Ephb6"         
## [11553] "Llcfc1"         "Gstk1"          "Casp2"          "Zyx"           
## [11557] "Or2a25"         "Or2a7"          "Prf1"           "Rny3"          
## [11561] "Zfp282"         "Zfp956"         "Krba1"          "Sspo"          
## [11565] "Atp6v0e2"       "Lrrc61"         "Repin1"         "Zfp775"        
## [11569] "Gimap4"         "Nodal"          "Gimap1"         "Tmem176a"      
## [11573] "Aoc1"           "Aoc1l2"         "Aoc1l1"         "Malsu1"        
## [11577] "Fam221a"        "Npy"            "Pals2"          "Gm56926"       
## [11581] "Lrrc20"         "Nfe2l3"         "Evx1"           "Tax1bp1"       
## [11585] "Prr15"          "Plekha8"        "Gars1"          "Mindy4"        
## [11589] "Ghrhr"          "Adcyap1r1"      "Avl9"           "Ppa1"          
## [11593] "Fkbp9"          "4930533I22Rik"  "Gm20673"        "Abcg2"         
## [11597] "Tigd2"          "Ccser1"         "Tnip3"          "4930544G11Rik" 
## [11601] "Mad2l1"         "Gm15644"        "Tysnd1"         "Serbp1"        
## [11605] "Igkv2-137"      "Eif2ak3"        "Gm1070"         "Cd8b1"         
## [11609] "Cd8a"           "Rnf103"         "Chmp3"          "Immt"          
## [11613] "Polr1a"         "Aifm2"          "0610030E20Rik"  "Tmem150a"      
## [11617] "Ggcx"           "Capg"           "Retsat"         "Gm15401"       
## [11621] "Suclg1"         "Gm6261"         "Gcfc2"          "Eva1a"         
## [11625] "4930507D05Rik"  "Gm31861"        "M1ap"           "Pcgf1"         
## [11629] "1700003E16Rik"  "Dctn1"          "Mob1a"          "Bola3"         
## [11633] "B230319C09Rik"  "Vax2"           "Atp6v1b1"       "4933428P19Rik" 
## [11637] "Ankrd53"        "Nagk"           "Rpl18"          "Dysf"          
## [11641] "Npm3-ps1"       "Emx1"           "Smyd5"          "Tprkb"         
## [11645] "Figla"          "Tgfa"           "Ankrd17"        "Slc25a16"      
## [11649] "Snrpg"          "Tia1"           "Asprv1"         "Aak1"          
## [11653] "Nfu1"           "Efcc1"          "Gp9"            "Hmces"         
## [11657] "Gm5577"         "Gata2"          "Dna2"           "Dnajb8"        
## [11661] "Ruvbl1"         "Mgll"           "Gm15612"        "Tpra1"         
## [11665] "4933427D06Rik"  "Gm1965"         "Vmn1r40"        "BC048671"      
## [11669] "Uroc1"          "Pbld2"          "Klf15"          "Aldh1l1"       
## [11673] "Hdac11"         "Fbln2"          "Tmem43"         "Lsm3"          
## [11677] "Slc6a6"         "Ccdc174"        "Fgd5"           "Nr2c2"         
## [11681] "Atoh7"          "Slc25a26"       "Kbtbd8"         "Arl6ip5"       
## [11685] "Gpr27"          "Btf3-ps6"       "Gxylt2"         "Ppp4r2"        
## [11689] "Cntn6"          "Trnt1"          "Setmar"         "Dnajc12"       
## [11693] "Edem1"          "Gm15519"        "Thumpd3"        "Mtmr14"        
## [11697] "Brpf1"          "Ogg1"           "Ttll3"          "Jagn1"         
## [11701] "Il17re"         "Il17rc"         "Jmjd1c"         "Creld1"        
## [11705] "Fancd2"         "Brk1"           "Irak2"          "Slc6a11"       
## [11709] "Slc6a1"         "Hrh1"           "Atg7"           "Pparg"         
## [11713] "D830050J10Rik"  "Egr2"           "Rho"            "H2az1"         
## [11717] "Zfand4"         "Or6d12"         "Or6d13"         "Or6d14"        
## [11721] "Cxcl12"         "Zfp637"         "Zfp239"         "Gm4875"        
## [11725] "Rhobtb1"        "Dcp1b"          "Cacna2d4"       "Fbxl14"        
## [11729] "Gm15532"        "Tuba8"          "A2m"            "1700063H04Rik" 
## [11733] "Nanog"          "Foxj2"          "Necap1"         "Ank3"          
## [11737] "C1rl"           "C1ra"           "Cdca3"          "Pianp"         
## [11741] "Zfp384"         "Ing4"           "Acrbp"          "Lpar5"         
## [11745] "Chd4"           "Nop2"           "Ccdc6"          "Iffo1"         
## [11749] "Mrpl51"         "Vamp1"          "Scnn1a"         "Tnfrsf1a"      
## [11753] "Ano2"           "D6Wsu163e"      "Gm43124"        "Fgf23"         
## [11757] "Gm4968"         "Mtif2"          "Mrln"           "Parp11"        
## [11761] "Cracr2a"        "Tspan11"        "Nrip2"          "Gm10069"       
## [11765] "Clec2h"         "Clec2d"         "Gabarapl1"      "Mir680-1"      
## [11769] "Prp2"           "Slc16a9"        "Smim10l1"       "Gm34149"       
## [11773] "Etv6"           "Bcl2l14"        "Borcs5"         "Cdkn1b"        
## [11777] "Apold1"         "Ddx47"          "Fam234b"        "Gm15476"       
## [11781] "Fam13c"         "Gm55605"        "Atf7ip"         "BC049715"      
## [11785] "Pde6h"          "Ptpro"          "Dera"           "Mgst1"         
## [11789] "Pyroxd1"        "Golt1b"         "Cmas"           "4930533K18Rik" 
## [11793] "Gm7457"         "D6Ertd474e"     "Etfrf1"         "1700073E17Rik" 
## [11797] "Rassf8"         "Sspn"           "Fgfr1op2"       "Med21"         
## [11801] "Stk38l"         "Gm6266"         "Etv5"           "Bmal2"         
## [11805] "Ppfibp1"        "Rep15"          "Mrps35"         "Ccdc91"        
## [11809] "Far2"           "Rps4l"          "Etfbkmt"        "Nacc1"         
## [11813] "Bicd1"          "Zwint"          "Samd9l"         "Calcr"         
## [11817] "Tfpi2"          "Bet1"           "Sgce"           "Gmfg"          
## [11821] "Pon3"           "Pon2"           "Pdk4"           "Rps27a"        
## [11825] "Pcdh15"         "Sem1"           "Rnps1"          "Gm16042"       
## [11829] "Thsd7a"         "Tmem168"        "Samtor"         "Asz1"          
## [11833] "Cttnbp2"        "Tspan12"        "Fam3c"          "Gm5778"        
## [11837] "Aass"           "Fezf1"          "Rnf148"         "Iqub"          
## [11841] "Ndufa5"         "Gm5302"         "Gpr37"          "Pot1a"         
## [11845] "Zfp800"         "Gcc1"           "Rab36"          "Lrrc4"         
## [11849] "Rbm28"          "Impdh1"         "Kcp"            "1700080G18Rik" 
## [11853] "Gm55823"        "Zc3hc1"         "Cep41"          "Tsga13"        
## [11857] "Klf14"          "Bcr"            "Lncpint"        "Plxna4"        
## [11861] "Chchd3"         "Npn2"           "Wdr91"          "Cnot4"         
## [11865] "Slc13a4"        "9330158H04Rik"  "Ybx1"           "Zc3hav1l"      
## [11869] "Copa"           "Specc1l"        "Zc3hav1"        "Hipk2"         
## [11873] "Kdm7a"          "Slc37a3"        "Mrps33"         "Dennd11"       
## [11877] "Try5"           "Prss3"          "Fam131b"        "Epha1"         
## [11881] "Gm5779"         "Or2r11"         "Tcaf1"          "Tpk1"          
## [11885] "Ezh2"           "Rny1"           "Pdia4"          "Rpl35a"        
## [11889] "Zfp777"         "Zfp746"         "Rarres2"        "Ggt5"          
## [11893] "Tmem176b"       "Tra2a"          "Npvf"           "Gm32479"       
## [11897] "Hnrnpa2b1"      "Skap2"          "Hoxa4"          "Hoxa5"         
## [11901] "Hoxa6"          "Hoxa7"          "Gm19326"        "Hoxa9"         
## [11905] "Mir196b"        "Jazf1"          "Cpvl"           "Scrn1"         
## [11909] "Fkbp14"         "Ggct"           "Crhr2"          "Lsm5"          
## [11913] "Kbtbd2"         "Derl3"          "Nt5c3"          "Ppm1k"         
## [11917] "Gprin3"         "Gm22622"        "Gm22723"        "Snca"          
## [11921] "Mageb16"        "Gadd45a"        "Igkv4-86"       "Rprl1"         
## [11925] "Chchd10"        "Spmip9"         "Thnsl2"         "Gm38828"       
## [11929] "Rmnd5a"         "Mrpl35"         "Ptcd3"          "Atoh8"         
## [11933] "Vamp8"          "Sh2d6"          "Elmod3"         "Vpreb3"        
## [11937] "Tcf7l1"         "Kcmf1"          "Tmsb10"         "Gm24533"       
## [11941] "Dnah6"          "Gm9001"         "Ctnna2"         "Mrpl19"        
## [11945] "Hk2"            "Tlx2"           "Gm5134"         "Wbp1"          
## [11949] "Wdr54"          "Mthfd2"         "Tet3"           "Dguok"         
## [11953] "Actg2"          "Stambp"         "Clec4f"         "Tex261"        
## [11957] "Gm7443"         "Zfp280b"        "Paip2b"         "Gm10445"       
## [11961] "Gm5878"         "Spr"            "Rab11fip5"      "Pradc1"        
## [11965] "Fbxo41"         "Egr4"           "Nat8f5"         "Nat8"          
## [11969] "S100b"          "Nat8f4"         "Dusp11"         "Pcyox1"        
## [11973] "Pcbp1"          "Mxd1"           "Gkn1"           "Aplf"          
## [11977] "Cfap92"         "Isy1"           "Rps19-ps9"      "Zkscan3"       
## [11981] "Gm9744"         "H1f10"          "1700031F10Rik"  "Eefsec"        
## [11985] "Sec61a1"        "Abtb1"          "Podxl2"         "Plxna1"        
## [11989] "Vmn1r-ps25"     "Vmn1r43"        "Chst13"         "2610028H24Rik" 
## [11993] "Cfap100"        "Iqsec1"         "Nup210"         "Wnt7a"         
## [11997] "Chchd4"         "Grip2"          "Mrps25"         "Rbsn"          
## [12001] "Trh"            "Prickle2"       "Lss"            "Adamts9"       
## [12005] "Magi1"          "Nup50l"         "Tafa4"          "Eogt"          
## [12009] "Tmf1"           "Uba3"           "Frmd4b"         "Gm25852"       
## [12013] "Gm23510"        "Spatc1l"        "Foxp1"          "Eif4e3"        
## [12017] "Prok2"          "Rybp"           "Ddx3x"          "Sumf1"         
## [12021] "5031434C07Rik"  "Ssu2"           "Oxtr"           "Rad18"         
## [12025] "Ftcd"           "Srgap3"         "Lhfpl4"         "Camk1"         
## [12029] "Tada3"          "Rpusd3"         "Fancd2os"       "Ghrl"          
## [12033] "Sec13"          "Atp2b2"         "Vgll4"          "Gm10787"       
## [12037] "Tamm41"         "Raf1"           "Gm14335"        "Snora7a"       
## [12041] "Efcab12"        "Mbd4"           "Plxnd1"         "Or6d15"        
## [12045] "Zfp422"         "Rassf4"         "Slc19a1"        "Tmem72"        
## [12049] "Rpl28-ps4"      "4933440N22Rik"  "Fxyd4"          "Csgalnact2"    
## [12053] "Ret"            "Bms1"           "Zfp248"         "Ankrd26"       
## [12057] "Lrtm2"          "Pofut2"         "Wnt5b"          "Erc1"          
## [12061] "Wnk1"           "Ccdc77"         "Tmem121b"       "Hdhd5"         
## [12065] "Atp6v1e1"       "Mical3"         "Phc1"           "C3ar1"         
## [12069] "Ube2g2"         "1700013D24Rik"  "Pex5"           "Emg1"          
## [12073] "Mir200c"        "Ptpn6"          "Grcc10"         "Atn1"          
## [12077] "Tpi1"           "Usp5"           "Gnb3"           "Krtap12-23"    
## [12081] "Gpr162"         "Lag3"           "Cops7a"         "Ncapd2"        
## [12085] "Tapbpl"         "Tuba3a"         "Ltbr"           "Cd9"           
## [12089] "Ndufa9"         "Rad51ap1"       "Sec22b"         "Krtap12-21"    
## [12093] "Tigar"          "Ccnd2"          "Gm7308"         "Gm55163"       
## [12097] "Gm10010"        "Tead4"          "Tulp3"          "Rhno1"         
## [12101] "Itfg2"          "Fkbp4"          "Krtap10-10"     "Pzp"           
## [12105] "Gm8724"         "Clec12b"        "Klra5"          "Magohb"        
## [12109] "Ybx3"           "Gm22362"        "Tas2r117"       "Gm5886"        
## [12113] "Gm8956"         "Cfap410"        "Lrp6"           "Dusp16"        
## [12117] "Gsg1"           "Pbp2"           "Ube2q2l"        "Gm6728"        
## [12121] "Plbd1"          "H4c16"          "Wbp11"          "Mgp"           
## [12125] "Dnmt3l"         "Erp27"          "Arhgdib"        "Rerg"          
## [12129] "Eps8"           "Igbp1b"         "Plcz1"          "Slco1a4"       
## [12133] "Ldhb"           "Abcc9"          "St8sia1"        "Cstb"          
## [12137] "C2cd5"          "Sox5"           "Dnai7"          "Kras"          
## [12141] "Lmntd1"         "Bhlhe41"        "Ints13"         "Tm7sf3"        
## [12145] "Pthlh"          "Ergic2"         "Gm5951"         "Gm55131"       
## [12149] "Dennd5b"        "Gm10388"        "Ndufa3"         "Prpf31"        
## [12153] "Cnot3"          "Tsen34"         "Rps9"           "Ttyh1"         
## [12157] "Leng8"          "Ilvbl"          "Lilra5"         "Atp6v0c-ps2"   
## [12161] "Brsk1"          "Nat14"          "Zfp524"         "Zfp865"        
## [12165] "Zfp580"         "Ccdc106"        "U2af2"          "Epn1"          
## [12169] "Cdc34"          "Rps18"          "Galp"           "Zfp78"         
## [12173] "Zfp28"          "Zfp264"         "Gm6909"         "Vmn2r-ps53"    
## [12177] "Zfp606"         "2900092C05Rik"  "Rps5"           "Bsg"           
## [12181] "Zfp324"         "Lig1"           "Phf20-ps"       "Phf20"         
## [12185] "Gm25354"        "Zfp541"         "Napa"           "Slc8a2"        
## [12189] "Meis3"          "Bbc3"           "Fgf22"          "Zc3h4"         
## [12193] "Tmem160"        "n-R5s151"       "Ap2s1"          "Slc1a5"        
## [12197] "Strn4"          "Dact3"          "Pnma8b"         "Pnma8a"        
## [12201] "Gm6065"         "Rbm42"          "Fstl3"          "Pglyrp1"       
## [12205] "Nova2"          "Mypop"          "Irf2bp1"        "Dmpk"          
## [12209] "Mir330"         "Gpr4"           "Opa3"           "Rtn2"          
## [12213] "Ercc1"          "Palm"           "Ppp1r13l"       "Ckm"           
## [12217] "Exoc3l2"        "Zfp296"         "Ceacam20"       "Nlrp4e"        
## [12221] "Nlrp5"          "Vmn1r179"       "Vmn1r181"       "Zfp180"        
## [12225] "Misp"           "Zfp114"         "Zfp108"         "Zfp93"         
## [12229] "Lypd5"          "Zfp428"         "Xrcc1"          "Phldb3"        
## [12233] "Dmrtc2"         "Rps19"          "Arhgef1"        "Ptbp1"         
## [12237] "Zfp574"         "D930028M14Rik"  "Zfp526"         "Prr19"         
## [12241] "Megf8"          "4732471J01Rik"  "Gm4607"         "Dmac2"         
## [12245] "B3gnt8"         "Exosc5"         "Cfd"            "Tgfb1"         
## [12249] "Gm55088"        "Cyp2f2"         "Actmap"         "Blvrb"         
## [12253] "Sertad3"        "Prx"            "2310022A10Rik"  "Ttc9b"         
## [12257] "Zfp626"         "Arid3a"         "Zfp607a"        "Fcgbpl1"       
## [12261] "Dyrk1b"         "Eid2b"          "Paf1"           "Ifnl3"         
## [12265] "Gm19880"        "Sycn"           "Sars2"          "Map4k1"        
## [12269] "Wdr18"          "Yif1b"          "Ppp1r14a"       "Dpf1"          
## [12273] "4930432E11Rik"  "Zfp84"          "Zfp568"         "Zfp260"        
## [12277] "Zfp382"         "Cox7a1"         "Polr2i"         "Grin3b"        
## [12281] "Clip3"          "Alkbh6"         "Syne4"          "Tyrobp"        
## [12285] "Arhgap33os"     "Hspb6"          "Igflr1"         "2200002J24Rik" 
## [12289] "Gm4883"         "Sbsn"           "Atp5f1d"        "Fam187b"       
## [12293] "Gm10640"        "Gm12755"        "Scgb1b27"       "Pepd"          
## [12297] "Cebpa"          "Rhpn2"          "Cep89"          "Slc7a9"        
## [12301] "B230322F03Rik"  "Midn"           "Ankrd27"        "E130304I02Rik" 
## [12305] "1600014C10Rik"  "Zfp939"         "Ube2h"          "Vstm2b"        
## [12309] "4930433I11Rik"  "Gm4884"         "Gm5592"         "Gm9246"        
## [12313] "Copg1"          "Cirbp"          "Gm15470"        "Zfp141"        
## [12317] "Gm19246"        "Gm7211"         "Gm9266"         "Siglecf"       
## [12321] "Siglecg"        "Lim2"           "Nkg7"           "Cldnd2"        
## [12325] "Fam174c"        "Etfb"           "Zfp719"         "Zfp819"        
## [12329] "Ctu1"           "Klk14"          "Klk12"          "Klk10"         
## [12333] "Klk4"           "Klk15"          "Klk1b7-ps"      "Pwwp3a"        
## [12337] "Klk1b8"         "Klk1b1"         "Klk1b9"         "Klk1b26"       
## [12341] "Klk1b27"        "Klk1b21"        "Klk1b22"        "Klk1b24"       
## [12345] "Klk1b4"         "Klk1b5"         "Ndufs7"         "Shank1"        
## [12349] "Syt3"           "Lrrc4b"         "Garin5a"        "Izumo2"        
## [12353] "Vrk3"           "Nup62"          "Il4i1"          "Akt1s1"        
## [12357] "Pnkp"           "Rps15"          "Tsks"           "Irf3"          
## [12361] "Rras"           "Nosip"          "Mir150"         "Pih1d1"        
## [12365] "Slc17a7"        "Pth2"           "Tead2"          "Slc6a16"       
## [12369] "Reep6"          "Rpl14-ps1"      "Ntf5"           "Lhb"           
## [12373] "Plekha4"        "Hsd17b14"       "Bcat2"          "Izumo1"        
## [12377] "Rasip1"         "Ntn5"           "Car11"          "Dot1l"         
## [12381] "Dbp"            "Fam83e"         "Lmtk3"          "Kdelr1"        
## [12385] "Odad1"          "Myod1"          "Kcnc1"          "Ifitm2"        
## [12389] "Ldhc"           "Tmem86a"        "Sf3a2"          "Zdhhc13"       
## [12393] "Nav2"           "Htatip2"        "Prmt3"          "4933405O20Rik" 
## [12397] "Ano5"           "Slc17a6"        "Gas2"           "Gm6181"        
## [12401] "Gm9367"         "Oaz1"           "Tubgcp5"        "Herc2"         
## [12405] "Oca2"           "Ndn"            "Magel2"         "Otud7a"        
## [12409] "Trpm1"          "Mir211"         "Mtmr10"         "Mcee"          
## [12413] "Tmprss9"        "Tars3"          "Pcsk6"          "Snrpa1"        
## [12417] "Selenos"        "Chsy1"          "Lins1"          "Cers3"         
## [12421] "Adamts17"       "Lysmd4"         "Igf1r"          "Psap"          
## [12425] "Gadd45b"        "Rgma"           "Fam174b"        "Gm10161"       
## [12429] "Akap13"         "Mrps11"         "Aen"            "Abhd2"         
## [12433] "Ticrr"          "9330171B17Rik"  "Mesp2"          "Thop1"         
## [12437] "Sema4b"         "Ngrn"           "Vps33b"         "Prc1"          
## [12441] "Hddc3"          "Zscan2"         "Slc28a1"        "Whamm"         
## [12445] "Sh3gl3"         "Efl1"           "Map2k2"         "Tmc3"          
## [12449] "2610206C17Rik"  "Vmn2r71"        "Grm5"           "Ctsc"          
## [12453] "Fzd4"           "Prss23os"       "Picalm"         "Sytl2"         
## [12457] "Ccdc89"         "Zbtb7a"         "Crebzf"         "Dlg2"          
## [12461] "Ccdc90b"        "Rab30"          "Prcp"           "Fam181b"       
## [12465] "Gm8309"         "Tenm4"          "Nars2"          "Gab2"          
## [12469] "Zfr2"           "Alg8"           "Ndufc2"         "Ints4"         
## [12473] "Gm24412"        "Rsf1"           "Clns1a"         "Pak1"          
## [12477] "Gdpd4"          "Thap12"         "Wnt11"          "Pip5k1c"       
## [12481] "Map6"           "Gdpd5"          "Gm56176"        "Arrb1"         
## [12485] "Mir326"         "Gm10605"        "Xrra1"          "C2cd3"         
## [12489] "Ucp2"           "Coa4"           "Cactin"         "Rab6a"         
## [12493] "Fam168a"        "Fchsd2"         "Arap1"          "Mir139"        
## [12497] "Clpb"           "Gm10602"        "Numa1"          "Art1"          
## [12501] "Pgap2"          "Tbxa2r"         "Stim1"          "Rrm1"          
## [12505] "Or52b3"         "Or51r1"         "Or52j3"         "Or52e3"        
## [12509] "Or52ab7"        "Usp17lc"        "Or52ae7"        "Gm15115"       
## [12513] "Mfsd12"         "Or51k2"         "Or51k7"         "Or52d1"        
## [12517] "Or52e7"         "Or52e5"         "Smpd1"          "Or2ag2b"       
## [12521] "Or10a5"         "Or2d36"         "Nlrp14"         "Dohh"          
## [12525] "Rbmxl2"         "Ppfibp2"        "Rbm3"           "Gm6007"        
## [12529] "Eif3f"          "Tub"            "Snora3"         "Akip1"         
## [12533] "Ipo7"           "Snora23"        NA               NA              
## [12537] NA               NA               NA               NA              
## [12541] NA               NA               NA               NA              
## [12545] NA               NA               NA               NA              
## [12549] NA               NA               NA               NA              
## [12553] NA               NA               NA               NA              
## [12557] NA               NA               NA               NA              
## [12561] NA               NA               NA               NA              
## [12565] NA               NA               NA               NA              
## [12569] NA               NA               NA               NA              
## [12573] NA               NA               NA               NA              
## [12577] NA               NA               NA               NA              
## [12581] NA               NA               NA               NA              
## [12585] NA
gene_ranks <- sort(gene_ranks[!is.na(names(gene_ranks))], decreasing = TRUE)

top_n <- 30

for (cat in categories) {
  gmt_file <- sprintf("../m5.go.%s.v2024.1.Mm.symbols.gmt", tolower(cat))
  
  if (file.exists(gmt_file)) {
    pathways <- gmtPathways(gmt_file)
    
    fgseaRes <- fgsea(pathways = pathways, stats = gene_ranks, minSize = 15, maxSize = 500)
    fgseaRes <- fgseaRes[order(fgseaRes$padj), ]
    fgseaRes$leadingEdge <- sapply(fgseaRes$leadingEdge, paste, collapse = "; ")
    
    write.csv(fgseaRes, sprintf("results/tables/fgsea_new_GO_%s.csv", cat), row.names = FALSE)
    
    fgsea_top <- head(fgseaRes, top_n)
    p_bubble <- ggplot(fgsea_top, aes(x = NES, y = reorder(pathway, NES), size = size, color = padj)) +
      geom_point() +
      scale_color_gradient(low = "red", high = "blue", name = "FDR") +
      scale_size(range = c(3, 10)) +
      labs(title = sprintf("Bubble Plot - Top Enriched Pathways (GO:%s)", cat), x = "NES", y = "Pathway") +
      theme_minimal(base_size = 12)
    print(p_bubble)
  } else {
    warning(sprintf("Plik %s nie znaleziony. Pomijam fgsea dla GO:%s.", gmt_file, cat))
  }
}
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.01% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.

gProfiler Analysis

if (length(de_genes) > 0) {
  
  gp <- gost(query = de_genes,
             organism = "mmusculus",
             sources = c("GO:BP", "GO:CC", "GO:MF", "KEGG", "REAC"),
             correction_method = "fdr",
             user_threshold = 0.05)
  
  gp_result_fixed <- gp$result
  list_cols <- sapply(gp_result_fixed, is.list)
  gp_result_fixed[list_cols] <- lapply(gp_result_fixed[list_cols], function(col) sapply(col, paste, collapse = "; "))
  
  if (!dir.exists("results/tables/")) dir.create("results/tables/", recursive = TRUE)
  if (!dir.exists("results/plots/")) dir.create("results/plots/", recursive = TRUE)
  
  write.csv(gp_result_fixed, "results/tables/gprofiler_enrichment_full.csv", row.names = FALSE)
  
  top_n <- 30
  sources <- c("GO:BP", "GO:CC", "GO:MF", "KEGG", "REAC")
  
  for (src in sources) {
    gp_src <- subset(gp_result_fixed, source == src)
    
    if (nrow(gp_src) > 0) {
      gp_top <- head(gp_src[order(gp_src$p_value), ], top_n)
      safe_src <- gsub("[:]", "_", src)
      
      write.csv(gp_src, sprintf("results/tables/gprofiler_%s_results_new.csv", safe_src), row.names = FALSE)
      
      p_bubble <- ggplot(gp_top, aes(x = -log10(p_value), y = reorder(term_name, -log10(p_value)),
                                     size = intersection_size, color = p_value)) +
        geom_point() +
        scale_color_gradient(low = "red", high = "blue", name = "p-value") +
        scale_size(range = c(3, 10), name = "Intersection Size") +
        labs(title = paste("gProfiler Bubble Plot -", src),
             x = "-log10(p-value)", y = "Term") +
        theme_minimal(base_size = 12)
      
      print(p_bubble)
    }
  }
  
} else {
  warning("Brak genów DE do analizy gProfiler.")
}

TopGO Analysis

gene_universe <- unique(na.omit(final_combined_unique$SYMBOL_final))
geneList <- factor(as.integer(gene_universe %in% de_genes))
names(geneList) <- gene_universe

ontologies <- c("BP", "MF", "CC")
top_n <- 30

for (ont in ontologies) {
  GOdata <- new("topGOdata",
                ontology = ont,
                allGenes = geneList,
                annot = annFUN.org,
                mapping = "org.Mm.eg.db",
                ID = "symbol")
  
  resultFisher <- runTest(GOdata, algorithm = "elim", statistic = "fisher")
  topgo_table <- GenTable(GOdata, Fisher.elim = resultFisher, topNodes = top_n)
  
  topgo_table$Fisher.elim <- as.numeric(sub("<", "", topgo_table$Fisher.elim))
  topgo_table$Fisher.elim[is.na(topgo_table$Fisher.elim)] <- 1  #' dla wartości "<1e-30"
  
  write.csv(topgo_table, sprintf("results/tables/topGO_%s_results_new.csv", ont), row.names = FALSE)
  
  p_bubble <- ggplot(topgo_table, aes(x = -log10(Fisher.elim), y = reorder(Term, -log10(Fisher.elim)),
                                      size = Significant, color = Fisher.elim)) +
    geom_point() +
    scale_color_gradient(low = "red", high = "blue", name = "p-value") +
    scale_size(range = c(3, 10), name = "Significant Genes") +
    labs(title = paste("topGO:", ont, "- Bubble Plot"), x = "-log10(p-value)", y = "GO Term") +
    theme_minimal(base_size = 12)
  
  print(p_bubble)
  
  pdf(sprintf("results/plots/topGO_GOgraph_%s.pdf", ont), width = 8, height = 10)
  showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 10, useInfo = "all")
  dev.off()
}
## 
## Building most specific GOs .....
##  ( 10785 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13945 GO terms and 30776 relations. )
## 
## Annotating nodes ...............
##  ( 11060 genes annotated to the GO terms. )
## 
##           -- Elim Algorithm -- 
## 
##       the algorithm is scoring 2236 nontrivial nodes
##       parameters: 
##           test statistic: fisher
##           cutOff: 0.01
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  19 nodes to be scored   (0 eliminated genes)
## 
##   Level 13:  31 nodes to be scored   (0 eliminated genes)
## 
##   Level 12:  72 nodes to be scored   (11 eliminated genes)
## 
##   Level 11:  122 nodes to be scored  (20 eliminated genes)
## 
##   Level 10:  200 nodes to be scored  (48 eliminated genes)
## 
##   Level 9:   270 nodes to be scored  (57 eliminated genes)
## 
##   Level 8:   311 nodes to be scored  (65 eliminated genes)
## 
##   Level 7:   331 nodes to be scored  (87 eliminated genes)
## 
##   Level 6:   359 nodes to be scored  (112 eliminated genes)
## 
##   Level 5:   279 nodes to be scored  (604 eliminated genes)
## 
##   Level 4:   163 nodes to be scored  (669 eliminated genes)
## 
##   Level 3:   57 nodes to be scored   (669 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (669 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (669 eliminated genes)

## 
## Building most specific GOs .....
##  ( 3832 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4304 GO terms and 5602 relations. )
## 
## Annotating nodes ...............
##  ( 10907 genes annotated to the GO terms. )
## 
##           -- Elim Algorithm -- 
## 
##       the algorithm is scoring 557 nontrivial nodes
##       parameters: 
##           test statistic: fisher
##           cutOff: 0.01
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   37 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   64 nodes to be scored   (0 eliminated genes)
## 
##   Level 7:   88 nodes to be scored   (0 eliminated genes)
## 
##   Level 6:   101 nodes to be scored  (88 eliminated genes)
## 
##   Level 5:   109 nodes to be scored  (134 eliminated genes)
## 
##   Level 4:   96 nodes to be scored   (146 eliminated genes)
## 
##   Level 3:   40 nodes to be scored   (207 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (207 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (207 eliminated genes)

## 
## Building most specific GOs .....
##  ( 1667 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1830 GO terms and 2984 relations. )
## 
## Annotating nodes ...............
##  ( 11109 genes annotated to the GO terms. )
## 
##           -- Elim Algorithm -- 
## 
##       the algorithm is scoring 338 nontrivial nodes
##       parameters: 
##           test statistic: fisher
##           cutOff: 0.01
## 
##   Level 11:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  26 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   43 nodes to be scored   (14 eliminated genes)
## 
##   Level 8:   48 nodes to be scored   (14 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (14 eliminated genes)
## 
##   Level 6:   60 nodes to be scored   (14 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (14 eliminated genes)
## 
##   Level 4:   26 nodes to be scored   (14 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (786 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (786 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (786 eliminated genes)

####################